Integrated optics fiber array

ABSTRACT

The device for detecting the binding of two chemical species includes a first plate having a base, multiple optical fibers and a second plate. The base has multiple grooves formed therein. The multiple optical fibers are each disposed within a corresponding one of the multiple grooves. The second plate has multiple channels formed therein. The first plate and the second plate are configured to be placed adjacent to one another such that each the optical fiber is exposed to and traverses the multiple channels.

This application claims the benefit of prior U.S. application Ser. No.10/602,900, filed Jun. 23, 2003, which application is a divisionalapplication of U.S. application Ser. No. 09/590,761, filed June 8, 2000,now U.S. Pat. No. 6,649,404, issued Nov. 18, 2003, which application isa divisional of U.S. application Ser. No. 09/479,181, filed Jul. 7,2000, now U.S. Pat. No. 6,635,470, issued Oct. 21, 2003 whichapplication is a continuation-in-part application of U.S. applicationSer. No. 09/227,799, filed Jan. 8, 1999, now abandoned, whichapplications are incorporated herein by reference in their entirety.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The invention relates generally to the detection of contact or bindingof chemical species. More specifically, the invention relates to asystem and method for contacting an oligonucleotide probe with anoligonucleotide target and for detecting such contact.

2. Description of Related Art

Presently, DNA micro-arrays or DNA (gene) chips are used for a widerange of applications such as gene discovery, disease diagnosis, drugdiscovery (pharmacogenomics) and toxicological research(toxicogenomics). Typically, an array of immobilized chemical compoundsor probes are contacted with a target of interest to identify thosecompounds in the array that bind to the target, thereby makingidentification of the target possible.

Existing methods for manufacturing these micro-arrays generallyinclude: 1) in-situ methods where multiple compounds are synthesizeddirectly onto a substrate to form a high density micro-array or 2)deposition methods in which pre-synthesized compounds are covalentlyattached to the surface of the substrate at the appropriate spatialaddresses by sophisticated robot dispensing devices. However, thein-situ method typically requires specialized reagents and complexmasking strategies, and the deposition method typically requires complexrobotic delivery of precise quantities of reagents.

Accordingly, existing methods for manufacturing micro-arrays are complexand expensive. As a result, there is a need for a simple andcost-effective high-throughput system and method for detecting thebinding of chemical species.

BRIEF SUMMARY OF THE INVENTION

According to some embodiment, there is provided an integrated opticsdevice for detecting the binding of two chemical species. The deviceincludes a first plate having a base, multiple optical fibers and asecond plate. The base has multiple grooves formed therein. The multipleoptical fibers are each disposed within a corresponding one of themultiple grooves. The second plate has multiple channels formed therein.The first plate and the second plate are configured to be placedadjacent to one another such that each optical fiber is exposed to andtraverses the multiple channels.

The device for detecting the binding of two chemical species can be usedto analyze multiple targets, is flexible, has multi-uses, is simple tomanufacture and use, and is less complex and less costly to manufactureand use then current systems and methods.

According to another embodiment of the invention there is provided amethod for making the integrated optics device for detecting the bindingof two chemical species. Each of a plurality of known chemical speciesare immobilized on a separate optical fiber of multiple optical fibers.Each optical fiber is disposed within a corresponding one of multiplegrooves formed in a first plate. A second plate is formed havingmultiple channels formed therein adjacent to the first plate such thateach the optical fiber is exposed to and traverses the multiplechannels.

According to yet another embodiment of the invention there is provided amethod for using the integrated optics device for detecting the bindingof two chemical species. A second plate having multiple channels formedtherein is placed adjacent to a first plate. The first plate has aplurality of immobilized chemical species each immobilized on a separateoptical fiber of multiple optical fibers. Each optical fiber is disposedwithin a corresponding one of multiple grooves formed in the firstplate. Each optical fiber is exposed to and traverses the multiplechannels. Each of a plurality of mobile chemical species is thendeposited into a separate one of the channels. The mobile chemicalspecies then contact the immobilized chemical species. Finally, it isdetected whether binding occurs between at least one of the mobilechemical species and at least one of the immobilized chemical species.

According to another embodiment of the invention there is provided aportable detector for detecting the binding of two chemical species. Theportable detector includes a support, a light source, a detector, and ahousing. The support is configured to receive a fiber array thereon. Thefiber array comprises multiple optical fibers. The light source isconfigured to direct light at an end of each of the multiple opticalfibers. The detector is configured to detect light emitted from at leastone of the multiple optical fibers caused by binding of two chemicalspecies. The portable detector is configured to be carried by hand.

Alternatively, the portable detector includes a fiber array, a housing,a light source and a detector. The fiber array includes a plate havingmultiple channels therein. The multiple optical fibers are disposed onthe support across the channels. Each of the multiple optical fibers hasan immobilized chemical species thereon. The housing is configured toreceive the fiber array therein. The light source is coupled to thehousing. The light source is configured to direct light at an end ofeach of the multiple optical fibers. The detector is coupled to thehousing The detector is configured to detect light emitted from at leastone of the multiple optical fibers caused by binding of two chemicalspecies.

According to one other embodiment of the invention there is provided adevice for contacting at least two chemical species. The device includesa plate, a fiber, and a molecular beacon. The plate includes a channelcapable of receiving a mobile chemical species. The fiber has animmobilized chemical species disposed along a portion of the fiber. Thefiber is disposed on the plate across a width of the channel such thatthe portion of the fiber is exposed to the channel. The molecular beaconis coupled to the mobile or the immobilized chemical species.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a top plan view of a fiber array according to the presentinvention;

FIG. 2 is a cross-sectional view along line 2-2 of the fiber array ofFIG. 1 according to the present invention;

FIG. 3 is a cross-sectional view along line 3-3 of the fiber array ofFIG. 1 according to the present invention;

FIG. 4 is a top plan view of another embodiment of a fiber arrayaccording to the present invention;

FIG. 5 is a cross-sectional view along line 5-5 of the fiber array ofFIG. 4 according to the present invention;

FIG. 6 is a cross-sectional view of another embodiment of the fiberarray 10A of FIG. 4;

FIG. 7 is a cross-sectional view along line 6-6 of the fiber array ofFIG. 4 according to the present invention;

FIG. 8 is a top plan view of a device for moving the fluid through thechannels of a fiber array according to the present invention;

FIG. 9 is a top plan view of another embodiment of a fiber arrayaccording to the present invention;

FIG. 10 is a cross-sectional view of a fluid dispensing device for use athe fiber array according to the present invention;

FIG. 11 is a perspective view of a portion of another embodiment of afiber array according to the present invention;

FIG. 11A is a perspective view of a portion of yet another embodiment ofa fiber array according to the present invention;

FIG. 12 is a schematic of an embodiment of a fiber array readeraccording to the present invention;

FIG. 13 is a schematic of the interface between the light source and thefiber shown in FIG. 11;

FIG. 14 is a perspective view of an embodiment of a plurality ofchannels used in a fiber array according to the present invention;

FIG. 15 is an end view of another embodiment of a plurality of channelsused in a fiber array according to the present invention;

FIG. 16 is an side view of the embodiment shown in FIG. 14;

FIG. 17 is another embodiment of a fiber array reader according to thepresent invention;

FIG. 18 is yet another embodiment of a fiber array reader according tothe present invention;

FIG. 19 is another embodiment of a fiber array according to the presentinvention;

FIG. 20 is a perspective view of a wheel according to one embodiment ofthe present invention;

FIG. 21 is a perspective view of a cylinder according to one embodimentof the present invention;

FIG. 22 is a cross-sectional view of a wheel coupled to a wheel rotationdevice according to one embodiment of the present invention;

FIG. 23 is a cross-sectional view of a container coupled to a containerrotation device according to one embodiment of the present invention;

FIG. 24 is a cross-sectional view of a fluid delivery system accordingto one embodiment of the present invention;

FIG. 25 is a cross-sectional view of a fiber wheel mixing systemaccording to one embodiment of the present invention;

FIG. 26 is a top plan view of the fiber wheel mixing system of FIG. 25;

FIG. 27 is a light evaluating system according to one embodiment of thepresent invention;

FIG. 28 is another embodiment of the light evaluating system of FIG. 27;

FIG. 29 is yet another embodiment of a light evaluating system accordingto the present invention;

FIG. 30 is a cross-sectional view of another embodiment of a fiber wheelmixing system including a wheel assembly and a multi-cavity containeraccording to the present invention;

FIG. 31 is another cross-sectional view of the fiber wheel mixing systemof FIG. 30;

FIG. 32 shows one embodiment for preparing a fiber for use in a fiberarray according to the present invention;

FIG. 33 shows another embodiment for preparing a fiber for use in thefiber array according to the present invention;

FIG. 34 is a diagrammatic view of the invention;

FIG. 35 is a side view of one embodiment of the invention;

FIG. 36 is a side view of another embodiment of the invention;

FIG. 37 is a side view of yet another embodiment of the invention;

FIG. 38 is a perspective view of an embodiment of the invention;

FIG. 39 is an enlarged perspective view of the fiber cutting deviceillustrated in FIG. 38;

FIG. 40 is a side view of the coating module illustrated in FIG. 38;

FIG. 41 is a side view of the stacked coating modules illustrated inFIG. 38;

FIG. 42 is an enlarged side view of the deprotection module illustratedin FIG. 38;

FIG. 43 is an enlarged side view of another embodiment of a coatingmodule according to the present invention;

FIG. 44 is a perspective view of the embodiment of the inventionillustrated in FIG. 43.

FIGS. 45A and 45B are partial perspective views of a fiber array plate,according to an embodiment of the invention;

FIG. 46A is an isometric view of a channel plate 4602;

FIG. 47 is a schematic of a fiber array system that uses molecularbeacons, according to another embodiment of the invention; and

FIG. 48 is a perspective view of a portable detector, according toanother embodiment of the invention.

DETAILED DESCRIPTION OF THE INVENTION

The system and method of the present invention provides a simple andreliable system for detecting the binding of at least two chemicalspecies. For a better understanding of the nature and objects of theinvention, reference should be made to the following detaileddescription taken in conjunction with the accompanying drawings. Likereference numerals refer to corresponding parts throughout the severalviews of the drawings.

The fiber array of the present invention provides a simple and reliablesystem for contacting at least two chemical species. Through the use offibers, the fiber arrays of the invention provide myriad advantages overcurrently available micro-arrays. For example, fibers having one or aplurality of chemical species immobilized thereon can be prepared inadvance and stored, thereby permitting rapid assembly of customizedarrays. Quite significantly, customized arrays comprising differenttypes of chemical species can be prepared as conveniently and rapidly asarrays comprised of a single type of chemical species.

Moreover, the arrays of the invention provide reliability that ispresently unattainable in the art. For the conventional described above,verifying the integrity of the array prior to use is virtuallyimpossible—chemical species immobilized at each spot in the array wouldhave to be individually analyzed—a task which would be quite laborintensive and, given the small quantities of chemical speciesimmobilized at a spot, may even be impossible. In the arrays of theinstant invention, the integrity of the chemical species immobilized ona fiber can be determined by simply analyzing a small portion of theentire fiber. Thus, through the use of fibers, the invention provides,for the first time, the ability to construct arrays of from a few to asmany as thousands, millions, or even billions of immobilized compoundsrapidly, reproducibly, and with a degree of fidelity that isunprecedented in the art.

In addition, because the chemistry for fabricating an array can beperformed in advance, the fiber array of the present invention alsoavoids wicking, cleaning, and on-line loading associated withimmobilizing the chemical with current deposition methods.

Construction of the fiber array is relatively simple. The placement ofthe fiber on the array is generally only sensitive in one direction,since each fiber can be placed anywhere along its axis. Spotting amicro-array, however, requires the handling of thousands of drops whichhave to be placed in very specific locations defined by two dimensions.Furthermore, spotting may result in contamination between contactpoints, whereas, fibers, each having different chemical speciesimmobilized thereon, may be placed next to each other with a reducedpotential for such contamination. In situ methods require thedevelopment of specialized chemistries and/or masking strategies. Incontrast, the arrays of the present invention do not suffer from thesedrawbacks. They can take advantage of well-known chemistries, and do notrequire deposition of precise volumes of liquids at definedxy-coordinates. The size of the fiber array of the present inventionalso allows for a large number of contact points with a relatively smallarray, thereby reducing the costs of making the array. The fiber arrayof the present invention also provides for a large number of contactpoints without the need for significant duplication.

Use of the fiber array of the present invention allows the firstchemical to be easily dispensed into channels in the array in order tocontact the fibers. In addition, different chemical species may bedispensed into each of the channels, which allows each contact point tobe unique. Further, fiber arrays of the present invention may providefor a relatively high signal to noise ratio, since the use of fiberswith optical properties allows for more controlled illumination of thecontact points. The fiber array of the present invention is particularlysuited for use in performing nucleic array by hybridization assays forapplications such as sequencing by hybridization and detectingpolymorphisms among others.

FIGS. 1-3 are various views of one embodiment of a fiber array accordingto the present invention. FIG. I is a top plan view of a fiber array 100comprising a support plate 102, a pair of end walls 104, 202 and aplurality of channel walls 106 which extend from one end of the supportplate 102 to the opposite end. The channel walls 106 form a plurality ofchannels 108, which also extend from one end of the support plate 102 tothe opposite end, for receiving a fluid containing a chemical species ofinterest. The channel walls 106 and the channels 108 may be essentiallyparallel.

The fiber array 100 further comprises a plurality of fibers 110 eachhaving immobilized thereon a chemical species of interest to becontacted with the chemical species dispensed in the channels 108. Thefibers 110 are disposed on the plurality of channel walls 106 such thateach fiber 110 is physically separated from each adjacent fiber 110. Thefibers 110 are placed in a position essentially parallel to each otherand essentially normal to the channels such that a portion of each fiber110 is in fluid contact with the fluid in each channel 108. Thisarrangement of the fibers 110 relative to the channels 108 effectivelycreates a matrix or array of contact points 112 or mix points betweenthe chemical species in the fluid in each of the channels 108 and thechemical species immobilized on each fiber 110.

FIG. 2 is a cross-sectional view along line 2-2 of FIG.1 of the fiberarray 100 according to the present invention. The channel walls 106 aredesigned to receive the fibers 110. As shown, the channel walls 106 havea groove 200 on top of the channel walls 106 to receive the fibers 110.This allows the fibers 110 to extend into the channels 108 to providefor direct contact between at least a bottom portion of each of thefibers 110 and the fluid in the channels 108. One of skill in the artwould recognize that a different geometry for the groove 200 can be usedbased upon the geometry of the fibers 110.

FIG. 3 is a cross-sectional view along line 3-3 of FIG. 1 of the fiberarray 100 according to the present invention. The channels 108 areformed by the channel walls 106 and the top of the support plate 102 andextend along the support plate 102 until terminated by end walls 104,202. Again, a bottom portion of each fiber 110 is exposed to eachchannel 108 such that placing a fluid in channel 108 will result incontact between the chemical species in the fluid and the chemicalspecies immobilized on each of the fibers 110.

The support plate 102, end walls 104, 202 and channel walls 106 may bemade of any material that is essentially inert to the chemical speciesof interest. One of ordinary skill in the art would be able to select anappropriate material for these features. In one embodiment the supportplate 102, end walls 104, 202 and channel walls 106 may be made of ahydrophobic material to reduce seepage of fluid through the channelwalls 106, thereby wetting only the fibers 110 and reducing the amountof fluid required. It should be appreciated that the dimensions of thesupport plate 102, end walls 104, 202 and channel walls 106, includingthe number of channels 108, may be altered depending upon the size ofthe array desired and the amount of fluid available to dispense in thechannels 108. However, it is important to keep the height of the channelwalls 106, the grooves 200, and the distance between the channel walls106 of such relative proportions to insure sufficient exposure of thesurface area of the fibers 110 to the fluid in the channels 108.Further, it should be appreciated that the thickness of the channelwalls 106 may also be altered to optimize the overall size of the fiberarray 100. Without limiting the dimensions of an array that could bemade according to the present invention, typical dimensions for thesupport plate may range froml cm to 1000 cm. The thickness of thechannel walls may range from 10 μm to 1000 μm, and the channel width mayrange from of 10 μm to 1000 μm. The height of the channel walls mayrange from 10 μm to 1000 μm.

The fiber 110 can be composed of virtually any material or mixture ofmaterials suitable for immobilizing the particular type of chemicalspecies. For example, as will be discussed in conjunction with FIG. 12,the fiber may be an electrically conductive wire. Alternatively, thefiber may be an optical fiber. Moreover, the use of the term “fiber” isnot intended to imply any limitation with respect to its composition ormaterials of construction or geometry. The fiber 110 will not melt,degrade, or otherwise deteriorate under the conditions used toimmobilize the chemical species or under the desired assay conditions.In addition, the fiber 110 should be composed of a material or mixtureof materials that does not readily release the immobilized chemicalspecies under the desired assay conditions. The actual choice ofmaterial will depend upon, among other factors, the identity of thechemical species immobilized and the mode of immobilization and will beapparent to those of skill in the art.

As will be discussed in more detail in conjunction with the preparationof the fiber 110, below, in embodiments employing covalent attachment ofthe chemical species, the fiber 110 is composed of a material or mixtureof materials that can be readily activated or derivatized with reactivegroups suitable for effecting covalent attachment. Non-limiting examplesof suitable materials include acrylic, styrene-methyl methacrylatecopolymers, ethylene/acrylic acid, acrylonitrile-butadiene-styrene(ABS), ABS/polycarbonate, ABS/polysulfone, ABS/polyvinyl chloride,ethylene propylene, ethylene vinyl acetate (EVA), nitrocellulose, nylons(including nylon 6, nylon 6/6, nylon 6/6-6, nylon 6/9, nylon 6/10, nylon6/12, nylon 11 and nylon 12), polycarylonitrile (PAN), polyacrylate,polycarbonate, polybutylene terephthalate (PBT), polyethyleneterephthalate (PET), polyethylene (including low density, linear lowdensity, high density, cross-linked and ultra-high molecular weightgrades), polypropylene homopolymer, polypropylene copolymers,polystyrene (including general purpose and high impact grades),polytetrafluoroethylene (PTFE), fluorinated ethylene-propylene (FEP),ethylene-tetrafluoroethylene (ETFE), perfluoroalkoxyethylene (PFA),polyvinyl fluoride (PVA), polyvinylidene fluoride (PVDF),polychlorotrifluoroethylene (PCTFE),polyethylene-chlorotrifluoroethylene (ECTFE), polyvinyl alcohol (PVA),silicon styrene-acrylonitrile (SAN), styrene maleic anhydride (SMA),metal oxides, and glass.

In some embodiments, the fiber 110 is an optical fiber. The opticalfiber is typically between about 10 μm and 1000 μm in diameter and canbe comprised of virtually any material so long as it is an opticalconductor at the wave length of interest. For example, the optical fibermay be an organic material such as polymethacrylate, polystyrene,polymethyl phenyl siloxane, or deuterated methyl methacrylate, or it maybe an inorganic material such as glass. In certain embodiments of theinvention, a beam of light directed through such optical fiber can beused to detect and/or quantify the interaction between the chemicalspecies in the fluid and the chemical species on the fibers (describedbelow).

It should be appreciated that each fiber 110 may actually contain adifferent chemical species, or multiple chemical species, in differentpositions along the fiber 110 or in multiple layers on the fiber 110.Therefore, the preparation of each fiber 110 and immobilization of thedesired chemical species thereto will vary depending upon the type offiber 110 used, the mode of immobilization, and the identity of thechemical species. Various methods for preparing fibers having a varietyof chemical species immobilized thereon are discussed in detail in alater section.

The number of fibers 10 comprising fiber array 100 will vary dependingupon the size of the matrix desired or the number of different chemicalspecies desired to be reacted with the chemical species in the channels108. The fibers 110 may be almost any length; however, the length issufficient to traverse all of the channels 108. It should beappreciated, however, that the fibers 110 may actually be of any length,diameter, or shape.

In general operation and use of the fiber array 100, a fluid containingone chemical species of interest is dispensed into the channels 108. Thefluid may be dispensed using any method known in the art for dispensinga fluid, such as pumping, aspirating, gravity flow, electrical pulsing,vacuum or suction, capillary action, or electro-osmosis. (One device fordispensing fluid onto the fiber array 100 is described below inconnection with FIG. 10.) Enough fluid is dispensed to insure contactwith a portion of some or all of the fibers 110. The fiber is contactedwith the fluid under conditions and for a period of time conducive topromoting interaction between the two chemical species. In instanceswhere excess chemical species in the fluid interferes with the detectionof the interaction, the fluid may be removed and the fibers optionallywashed prior to detection. The interaction, if any, between the chemicalspecies in the fluid and that on the fibers 110 is then analyzed at oneor more contact points 1 12.

In some instances such as assays involving hybridization of nucleicacids, it may be desirable to control the temperature of the fiber arrayduring the assay. This can be achieved using a variety of conventionalmeans. For example, if the device is constructed of an appropriateconductor, such as anodized aluminum, the device may be contacted withan appropriately controlled external heat source. In this instance, thefiber array would act essentially as a heat block. Alternatively, thechannels 108 could be outfitted with heaters and thermocouples tocontrol the temperature of the fluid disposed within the channels.

The method by which the interaction is analyzed will depend upon theparticular array. For example, where the two chemical species eachconstitute one member of a binding pair of molecules ( for example, aligand and its receptor or two complementary polynucleotides), theinteraction can be conveniently analyzed by labeling one member of thepair, typically the chemical species in solution, with a moiety thatproduces a detectable signal upon binding. Only those contact points 112where binding has taken place will produce a detectable signal.

Any label capable of producing a detectable signal can be used. Suchlabels include, but are not limited to, radioisotopes, chromophores,fluorophores, lumophores, chemiluminescent moieties, etc. The label mayalso be a compound capable of producing a detectable signal, such as anenzyme capable of catalyzing, e.g., a light-emitting reaction or acolorimetric reaction. The label may be a moiety capable of absorbing oremitting light, such as a chromophore or a fluorophore.

Alternatively, both chemical species are unlabeled and their interactionis indirectly analyzed with a reporter moiety that specifically detectsthe interaction. For example, binding between an immobilized antigen anda first antibody (or visa versa) could be analyzed with a labeled secondantibody specific for the antigen-first antibody complex. Forpolynucleic acids, the presence of hybrids could be detected byintercalating dyes, such as ethidium bromide, which are specific fordouble-stranded nucleic acids.

Those of skill in the art will recognize that the above-described modesof detecting an interaction between the two chemical species at acontact point are merely illustrative. Other methods of detecting myriadtypes of interactions between chemical species are well known in the artand can be readily used or adapted for use with the fiber arrays of thepresent invention.

It should be appreciated that since each channel 108 is fluidly isolatedfrom each other channel 108, a different chemical species may bedispensed into each channel 108. If each fiber 1 10 has a differentchemical species immobilized thereon, this would create a matrix ofcontact points 112 in which each contact point 112 is unique.Furthermore, in some embodiments, chemical species may be serially orsimultaneously dispensed into the same channels 108. Sequentialdispersing is particularly useful, for example, where the chemicalspecies immobilized on fiber 110 is synthesized in situ on the fiber110.

FIGS. 4-6 are various views of another embodiment of a fiber array 400according to the present invention. Fiber array 400 is similar to fiberarray 100, but with the addition of a cover plate 402. FIGS. 4-6 areessentially the same views as FIGS. 1-3, but show a cover plate 402. Itshould be appreciated that while a cover plate is convenient inoperation and use of the fiber array, it is not necessary.

FIG. 4 is a top plan view of fiber array 400, according the presentinvention. Cover plate 402 comprises a plurality of channel inlet ports404, which are each fluidly connected to separate channels 108 at oneend of the channels 108, and a plurality of channel outlet ports 406,which are also each fluidly connected to separate channels 108 at theopposite end of the channels 108. The channel inlet ports 404 provide anopening through which the fluid containing a chemical species ofinterest is dispensed into a respective channel 108. The channel outletports 406 allow the fluid to exit the fiber array 400. Similar to thesupport plate 102, cover plate 402 may be made of any material that isessentially inert to the chemical species of interest, and one ofordinary skill in the art would be able to select an appropriatematerial. Further, it should be appreciated that cover plate 402 may betransparent to facilitate detection of the interaction between thechemical species being contacted.

FIG. 5 is a cross-sectional view of the fiber array 400 along line 5-5of FIG. 4. The cover plate 402 comprises a pair of end walls 504, 506which mate with the end walls 104, 202, respectively, of the supportplate 102. The cover plate 402 further comprises a plurality of channelwalls 508 which also mate with the channel walls 106 to seal eachchannel 108 such that fluid cannot pass from one channel to another. Thechannel walls 508 also have grooves 510 for receiving the fibers 110.The channel walls 508 and the channel walls 106 also mate to enclose andsecure those portions of the fibers 110 laying within the grooves 510,200. It should be appreciated that the cover plate 402 may be secured tothe support plate 102 by any method for adhering two materials dependingupon their specific composition. For example, diffusion bonding, inertadhesives, laser or ultrasonic welding, or fasteners may all be used.Other methods for securing two structures together are well known in theart.

FIG. 6 is a cross-sectional view of the fiber array 400 along line 6-6of FIG. 4. The channels 108 extend above and below the fibers 110 suchthat the longitudinal portions of the fibers 110 exposed to the channels108 may be surrounded by the fluid introduced into the channels 108. Thechannel outlet ports 46 extend through the cover plate 42 to allow thefluid to pass from the channels 108 through the cover plate 42 and outof the fiber array 400. The channel inlet ports are constructed in asimilar fashion to allow the fluid to pass through the cover plate 42into the channels 108.

The operation and use of the fiber array 400 with the cover plate 402 isessentially the same as the fiber array 100 without the cover plate 402.However, the cover plate 402 fluidly seals each of the channels 108,thereby allowing for other methods to be used to move the fluid throughthe channels 108. For example, a pump may be used to pressurize thefluid in the channels 108, thereby forcing the fluid through thechannels. Alternatively, centrifugal force may be used to force thefluid through the channels.

FIG. 7 is a cross-sectional view of another embodiment of the fiberarray 400 of FIG. 4 illustrating a design for securing the fibers 110between the support plate and the cover plate. As shown, support plate700 comprises grooves 702 for receiving the fibers 110. Cover plate 704comprises a plurality of teeth 706 which correspond and mate with thegrooves 702. This configuration allows the cover plate to be more easilyaligned in securing it to the support plate 700, since any tooth 706 maybe mated with any groove 702. It should be appreciated that any designor shape for the teeth and the groove may be used. Moreover, it shouldbe appreciated that the fiber array 400 may be constructed withoutgrooves for securing the fibers 110, and the fibers may simply bepinched between the support plate and the cover plate upon securing thesupport plate to the cover plate.

FIG. 8 is a top plan view of a device for moving the fluid through thechannels 108 of the fiber array 400 having a cover plate 402. Rotatingplate 800 is any device which can be rotated about its center axis. Thefiber array 400 is secured to the rotating plate 800 such that thechannel inlet ports 404 are located near the center of the rotatingplate 800, and the channels 108 extend radially outward toward the outerperimeter of the rotating plate 800. The fiber array 400 may be securedto the rotating plate 800 by any means known in the art such as hooks,clips, screws, bolts, magnets and the like. As the rotating plate 800 isrotated about its axis, centrifugal force will move the fluid from theend of the channels 108 near the channel inlet ports 404 through thechannels 108 toward the channel outlet ports 406, thereby moving thefluid past each fiber 110. The channel outlet ports 406 may be sealed toprevent the fluid from exiting the fiber array during rotation. Itshould be recognized that additional fiber arrays may be placed on therotating plate 800 at the same time.

FIG. 9 is a top plan view of another embodiment of a fiber array 900according to the present invention. The fiber array 900 is similar tothe fiber array described in connection with FIGS. 1-8, comprising aplurality of fibers 110 and a plurality of channels 902 intersecting thefibers 110. The fibers 110 are essentially parallel to each other, andthe channels 902 are essentially perpendicular to the fibers 110. Thefiber array 900, however, additionally comprises a plurality of channelinlet ports 904 which are each connected to a respective channel inletline 906. Each channel inlet line 906 is connected to one end of arespective channel 902 and allows fluid to pass from each of the channelinlet ports 904 to its respective channel 902 within the fiber array900. The opposite end of each channel 902 is sealed.

The channel inlet ports 904 are arranged to facilitate dispensing thefluid into each channel inlet port 904 with ease and without resort totechniques and micro-sized equipment for dispensing fluid into extremelysmall openings. With a larger opening, each channel inlet port 904 canaccommodate a larger apparatus for dispensing fluid such as a pipette orsyringe, thereby reducing the error associated with the transfer ofsmall volumes of fluid.

To provide such larger openings, the channel inlet ports 904 arepositioned adjacent to the fiber array 900 and are connected to theirrespective channels 902 by a channel inlet line 906. FIG. 9 showsseveral groups of ten channel inlet ports 904, each arranged onalternating sides of the fiber array 900. Each channel inlet port 904within one group is offset in two directions from its adjacent channelinlet port 904. Specifically, each channel inlet port 904 is offset in adirection parallel to the channels by a distance equivalent to the sizeof the opening of the channel inlet port 904 and in a direction parallelto the fibers 110 by a distance equivalent to one channel width. Thisnecessitates that each channel inlet line 906 will be of increasinglength. However, in this manner the size of the channel inlet port 904can be maintained, as well as the alignment between the channel inletport 904, its respective channel inlet line 906 and its respectivechannel 902.

The channel inlet ports 904 are arranged in this fashion until the widthof all of the adjacent channel inlet ports 904 in one group, as measuredin a direction parallel to the fibers, is equivalent to the size of theopening of one channel inlet port 904. This arrangement of a group ofchannel inlet ports 904 is then repeated on the opposite side of thefiber array 900. This alternating arrangement of groups of channel inletports 904 and their respective channel inlet lines 906 can be continuedalong the fiber array 900 indefinitely. While this is one arrangement ofthe channel inlet ports 904 and their respective channel inlet lines906, it should be appreciated that the channel inlet ports 904 mayactually be positioned in any fashion along the fiber array 900.

It should be noted that the channels 902 are also positioned in analternating fashion corresponding to the groups of channel inlet lines906, since one end of each channel 902 is sealed. Therefore, inalternating fashion, a number of channels 902, equivalent to the numberof channel inlet lines 906, will have their open ends on one side of thefiber array 900 and the next group of channels 902 will have their openends on the other side of the fiber array 900. Further, since thechannels 902 are sealed at one end there is no channel outlet port.Therefore, in operation, a sufficient quantity of fluid is simplydispensed into the channel inlet ports 904 and is not removed from thechannels 902.

FIG. 10 is a cross-sectional view of a fluid dispensing device for usewith the fiber array 100 of FIGS. 1-3. The fluid dispensing device 1000comprises a fluid dispenser body 1002 which fixedly holds a plurality offluid dispensers 1004, each having a fluid dispenser opening 1006. Eachfluid dispenser 84 is aligned over a channel 108 such that there is onefluid dispenser 1004 for each channel 108. It should be appreciated,however, that a greater or lesser number of fluid dispensers 1004 may beused to feed additional channels or to provide more than one dispenserper channel. Fluid is fed to each fluid dispenser opening 1006 by afluid feed line 1008 which is fluidly connected to a fluid deliverysystem 1010. The fluid delivery system 1010 may be any system known inthe art that is capable of metering and delivering fluid to a fluidline, such as a pump, an aspirator, by capillary action, by moving agiven quantity of fluid from a reservoir through the fluid feed lines1008 and out of the fluid dispenser openings 1006. The fluid dispenseropenings 1006 permit the fluid to be disposed either into the channels108 or onto the fibers 110. The dispenser openings 1006 may be simplyopenings at the end of the fluid feed line 1008, nozzles, pipette tips,syringe or needle tips, capillary tubes, quills, or ink jets. Otherdevices through which a fluid is conveyed are well known in the art. Itshould be appreciated that the fluid delivery system 1010 should alsohave the capability of metering and delivering different fluids to eachof the fluid feed lines 1008. This permits the ability to contact eachof the fibers with a different chemical species.

The fluid dispenser body 1002 is connected to a motion device 1012 whichacts to move the fluid dispenser body 1002 in a direction parallel tothe channels 108. This permits the fluid dispensing device 1000 todispense fluid at various locations along each channel 108 or onto eachfiber 110. In addition, the motion device 1012 may move the fluiddispenser body 1002 in a direction parallel to the fibers. This allowsfor the use of fewer fluid dispensers 1004, since a given set of fluiddispensers 1004 may be moved and aligned to dispense fluid into anotherset of corresponding channels 108. The motion device 1012 may be anytype of mechanical device which operates to move an object within ahorizontal plane, such as a conveyor or a rotating screw system tocertain xy-coordinates. Motion devices of this type are well known inthe art.

In operation, a chemical species to be contacted with the chemicalspecies immobilized on the fibers 110 may be placed in a carrier fluidheld in a reservoir within the fluid delivery system 1010. Upon demand,for example by computer control, the fluid dispenser body 1002 is movedto a desired location above the fiber array 100, and the fluid deliverysystem 1010 delivers the fluid to the fluid dispensers 1004 andultimately to the respective channels 108 or onto the respective fibers110. Depending upon the geometry of the fiber array and the volume ofthe channels 108, the amount of fluid dispensed will vary; however, asufficient amount of fluid should be dispensed to insure adequatecontact with the fibers 110. The fluid dispenser body 1002 can then bemoved to another location, either along the same channel 108 or to adifferent channel 108 to dispense additional fluid. It should beappreciated that each fluid dispenser 1004 may dispense a differentfluid, or a second fluid may be dispensed after the first fluid isdispensed. In this latter case, rinsing of the fluid feed lines 1008 andthe fluid dispensers 1004 before dispensing the second fluid may beappropriate.

FIG. 11 is a perspective view of a portion of another embodiment of afiber array according to the present invention which useselectro-osmosis to move a fluid through the channels of the fiber arrayto assist in contacting the fluid and the fibers. The fiber array 1100is essentially the same as those previously described; however, thefibers 1110 are conductive. The fibers 1110 may be made conductive byapplying a conductive coating (not shown), which underlies the chemicalspecies (not shown) immobilized on the fibers 1110, such as silver orgold. Alternatively, the fibers 1110 may be made conductive byconstructing the fiber 1110 itself of a materially that is electricallyconductive and which optionally transmits light, such as indium tinoxide. A conductive contact 1116 surrounds the fibers 1110 at the edgeof the support plate 1118. The conductive contact 1116 serves as a meansfor electrically connecting a power supply 1124 to each of the fibers1110 using wires 1122. Wires 1126 connect the power supply 1124 to thefluid in channels 1120 thereby completing the circuit.

In operation, the fibers 1110 would be charged and made electricallyconductive by supplying power from the power supply 1124 to theconductive contact 1116 of each fiber 1110, and therefore, to theconductive coating of each fiber 1110. The fluid dispensed into thechannels 1120 would comprise, in addition to the chemical species ofinterest, an electrolyte that would be in contact with the power supply1124 using wires 1126, thereby completing the circuit. The applicationof power to the fibers 1110 causes the fluid containing the chemicalspecies of interest to move through the channel 1120 throughelectro-osmosis. Power may then be supplied to an adjacent fiber to movethe fluid further along the channel 1120. It should be appreciated thatpower may be supplied sequentially to single fibers or to groups offibers. It should also be appreciated that the voltage necessary forelectro-osmosis may vary with the electrolyte used, the chemical speciesof interest and the materials used to construct the channel walls, whichmay be non-conductive, such as glass or plastic. Typical voltagesapplied to the fibers may range from a few volts to several kilovolts.Therefore, power supply 1124 must be capable of providing such a rangeof voltages.

Additionally, electrophoretic forces may be used to provide a greaterdegree of contact between the chemical species of interest in the fluidand those immobilized on the fiber. Using the embodiment of FIG. 11, thepolarity of the fiber and the electrolytic fluid may be reversed usingthe power supply 1124 in an oscillating fashion at frequencies in thekilohertz range. By reversing the polarity in an alternating fashion,the chemical species of interest in the fluid may be drawn closer to thechemical species on the fiber and then pushed away in the event that thedesired interaction does not occur. The process of drawing the chemicalspecies in the fluid close to the fiber may increase the efficiency ofcontact between the chemical species. The process of pushing thechemical species in the fluid away from the fiber may increase theaccuracy of the interactions by reducing the number of falseinteractions wherein an interaction is detected due to non-specificbinding to the fiber, but not a true interaction between the chemicalspecies of interest. The voltages and oscillating frequencies necessaryto accomplish this will be dependent upon the composition of the fluidand the chemical species of interest. It should be appreciated, however,that the force used to push the chemical species in the fluid away fromthe fiber must not be so great as to disrupt a true interaction with thechemical species on the fiber. The use of electrophoresis is furtherdescribed in U.S. Pat. Nos. 5,605,662 and 5,632,957, both of which areincorporated herein by reference.

FIG. 11A is a perspective view of a portion of yet another embodiment ofa fiber array according to the present invention. In this embodiment,the wires 1122 may be positioned within the fluid at the end of thechannel distal from the end where wires 1126 are positioned. Both setsof wires 1122 and 1126 are connected to the power supply 1124, therebycompleting the circuit. In addition, it should be appreciated that theinvention may easily be adapted to provide a charged surface, using, forexample, a channel wall, that enables electro-osmosis orelectrophoresis.

As described above, the fiber array of the present invention is used tocontact at least two chemical species and to detect and/or quantify aninteraction between these species. One of skill in the art would be ableto select an appropriate detection method for use with the fiber arrayof the present invention, such as those previously described. In somecases, especially those instances where the interaction between thechemical species in solution and that immobilized on the fiber cause adifference in the absorbance or emission of light, such as thoseinstances where the chemical species disposed within the channels 108are labeled with a fluorophore, it is desirable to measure the amountand/or wavelength of light emanated from each of the contact points 112as a result of the interaction between the chemical species in thechannels 108 and on the fibers 110 using a light evaluating device suchas the human eye, a camera, or spectrometer. To accomplish this, theentire support plate 102 may be illuminated; however, this may createundesirable background illumination and reduce the signal to noise ratioin the light evaluating device. Therefore, it may be desirable to moreselectively illuminate a portion of the fiber array, for example asingle fiber or a group of fibers for evaluation, thereby providinggreater distinction between contact points 112.

FIG. 12 is a schematic of an embodiment of a fiber array reader 1200according to the present invention. The fiber array 1202 may be the sameas the fiber array 100 shown in FIGS. 1-3, the fiber array 400 having acover plate 402 as in FIGS. 4-6, or the fiber array 900 as in FIG. 9;however, the fibers 110 are optical fibers. For purposes of the presentinvention, an optical fiber is any material used as a fiber which istransparent to a given wavelength or wavelengths of light. The fiberarray reader 1200 consists of a light source 1204, such as an excitationlaser or an arc lamp, which produces a beam of light having the desiredwavelength, which is directed to the end of a fiber 110. A motion device1206 is used to move the light source 1204 and the fiber array 1202,relative to one another. Either the light source 1204 is moved, thefiber array 1202 is moved, or both are moved relative to one another bythe motion device 1206. Any motion device 1206 known in the art may beused such as a stepper motor or a conveyor powered by a reversible motorcapable of moving the conveyor back and forth. A motion detection systemwith motion sensors (not shown), such as infrared light sensors, may beused to monitor the position of the motion device 1206. The reader 1200may further comprise light evaluating devices or detectors 1208 whichmay comprise any device capable of receiving and at least qualitativelyevaluating light such as the human eye, a camera (e.g., confocal or CCDcamera) or a spectrometer. The detectors 1208 are positioned abovecontact or mix points 112 which occur at the intersection of the fibers110 and the channels 108. The reader 1200 may also include a heater 1212to ramp temperature as will be discussed infra in relation to FIG. 17.

In operation, a fluid is inserted into input holes 1210 at one end of achannel 108. The fiber 110 is thereby contacted with the fluidcontaining a chemical species under conditions conducive to interactionbetween the chemical species immobilized on fiber 110 and the chemicalspecies in solution. Each channel may receive a different or similarfluid.

FIG. 13 is a schematic view of the interface between the light source1204 and the fiber 110 shown in FIG. 12 once the fluid containing achemical species has contacted the fiber 110. The light source 1204generates light rays 1300 that are focused by a lens 1302 into an end ofa given fiber 110 (or group of fibers) and that reflect internallyinside of the fiber 110. The lens 1302 may be a cylindrical lens thatforms the rays 1300 into a focal point 1304 at the end of the fiber 110.The focal point 1304 may form a plane perpendicular to the fiber 110 sothat of the fiber 110 and the light source 1204 do not require exactalignment. The light reflecting inside the fiber 110 creates anevanescent wave 1306 on the surface of the fiber 110 illuminating thefiber surface. In a DNA hybridization application, the fluid containingthe chemical species or sample fragment 1308 could be a DNA fragmentlabeled with a fluoraphore. A probe DNA fragment 1310 is attached to thefiber 110 as explained supra. If the structure of the sample fragment1308 matches the structure of the probe DNA fragment 1310, the samplefragment 1308 will hybridize with the probe DNA fragment 1310 and remainat the fiber surface. Since the evanescent wave 1306 only illuminatesnear the fiber surface, the sample fragment 1308 labeled with thefluoraphore will be illuminated and fluoresce if hybridized to a probeDNA fragment 1310, while mismatch DNA will not hybridize and therefore,not fluoresce, since it is not near the fiber surface. Thus,hybridization of the sample fragment 1308 to a particular probe DNAfragment 1310 is indicated by the presence of fluorescent light when asample fragment 1308 is injected into the channel 108 and exposed to thefibers 110. If the interaction between the sample fragment 1308 and theprobe DNA fragment 1310 causes an increase or decrease in the absorbanceof a particular wavelength of light, the area around a contact point 112will emit either a greater or lesser quantity of light as compared withcontacts point 112 where no interaction occurred. The intensity of thisevanescent wave 1306 exponentially dissipates with distance from thesurface of the fiber 110 and almost disappears beyond 300 nanometers.Therefore, only the fiber 110, and the chemical species on the fiber,probe DNA fragment 1310, receiving the beam of light 1300 areilluminated. The material around the fiber 110 is not illuminated. Thus,the signal to noise ratio received by the light evaluating device ordetector is improved. Because of their selective illumination, theoptical fiber arrays of the invention can be advantageously used withassays where the chemical species in solution is labeled with afluorophore without first having to remove the excess, unreacted labeledspecies. The labeled species only produce a detectable fluorescencesignal if they interact with the chemical species immobilized on opticalfiber 110; labeled species free in solution are not illuminated and donot fluoresce. Of course, where desired, the excess unlabeled chemicalspecies can be removed prior to detection.

It should be appreciated that the wavelength of light used forilluminating the fibers will depend upon the optical absorption band ofthe fluorescent molecule. In addition, the light evaluating device needsto be able to detect the excitation light.

Referring to FIGS. 12 and 13, after measuring the light at a givencontact point 112, or set of contact points along a given fiber 110, orset of fibers, the light evaluating device 1208 may be moved, manuallyor automatically, to the next contact point 112, or set of contactpoints along the same fiber 110, or next set of fibers. Alternatively,there may be a light evaluating device 1208 fixed at each contact point112. Once all of the contact points 112 along a given fiber, or set offibers, have been evaluated, the motion device 1206 may move the lightsource 1204 and the focusing lens 1302 to the next fiber 110, or set offibers, such that the beam of light 1300 is aligned appropriately withthe end of the next fiber 110, set of fibers. Alternatively the lightevaluating device 1108 may be fixed, and the array 1102 may be moved asdescribed supra. It should be appreciated, however, that any contactpoint 112, or set of contact points may be evaluated in any sequence andin any time interval. One advantage of selectively illuminating certainfibers or groups of fibers, compared to illuminating the entire plate,is a reduction in noise from fibers and contact points that are adjacentto those being evaluated by the light evaluating device 1208. Thisreduces the potential confusion as to which contact points 112 are beingobserved.

FIG. 14 shows a perspective view of an embodiment of a channel 108 usedin a fiber array in connection with the use of a light source toilluminate the fibers 110. As shown, the bottom of the channel 108 hasmultiple curves positioned beneath where each fiber 110 would lay. Inaddition, the channel 108 may have a reflective coating 1400. Thecurvature of the bottom of the channel 108 and the reflective coating1400 act to reflect the light back towards the light evaluating deviceto improve the strength of the light signal received from each contactpoint. The reflective coating 1400 may be made from any material thatreflects light, such as, for example, aluminum, gold and mixturesthereof. Furthermore, the reflective coating 1400 may be multi-layered.It should be appreciated that while only one channel 108 is shown, eachchannel 108 may be similarly designed.

FIG. 15 is an end view of another embodiment of the channels 108 shownin FIG. 14, and FIG. 16 is a side view of the embodiment shown in FIG.15. The amount of fluorescent light 1500 collected into the detectoroptic 1502 can be increased by designing the curve of the channels 108to reflect light in a desired direction. One embodiment of a detectoroptic 1502 is a fiber optic with a much larger diameter than the fiber110. The detector optic 1502 directs the collected light intoa-photo-detector 1504, producing an electrical signal that isproportional to amount of light 1500. In some embodiments, thephoto-detector 1504 is a solid-state diode or a photo multiplier tube.The channel curving can be in all dimensions, and the reflectionefficiency may vary, but the general intent is to redirect light intothe detector optic 1502 that would otherwise be lost into the channelsubstrate 1506.

FIG. 17 is another embodiment of a fiber array reader 1700. Anelectrical signal is sent from a photo-detector 1702 through a cable1704 to an analog to digital converter 1706 where a digital signal isgenerated for interpretation and plotting by a computer 1708. Forexample, the signal data 1722 could be plotted as intensity 1710 overtime 1712. The fiber array 1714 can be arranged in a circulararrangement as shown to allow for continuous reading of the fibers 110.A motor 1716 rotates a hub 1718, supporting the fiber array 1714, atsome specified rate, such as for example one revolution per second. Alaser 1720 is fixed such that the light from laser 1720 forms a focusedline at the fiber-end, as discussed supra. In other words, the fibers110 are sequentially rotated into the focused line of laser light.Because the laser line or plane is much narrower than the spacingbetween the fiber's 110 diameters, the fibers need not be accuratelyplaced along that line for the light to enter the fiber. Furthermore,the fibers need not be accurately aligned in the orthogonal dimensioneither, as the fibers 110 are guaranteed to rotate into a fixed line oflight.

A heater/cooler 1724 uniformly controls the temperature of the fiberarray 1714. The signal from each fiber 110 is analyzed each rotation ofthe hub 1718 and a plot for each fiber mix-point is generatedindependent of any other fiber. Furthermore, the temperature is rampedover a range guaranteed to pass though the optimum temperature forbinding of a mobile and an immobilized chemical species. The optimumtemperature for DNA hybridization is the optimum hybridizationtemperature for that particular probe, as each probe has a differentoptimum hybridization temperature. Thus, each probe is observed at itsoptimum hybridization even though each probe in the fiber array 1714 hasa different optimum hybridization temperature.

FIG. 18 shows yet another embodiment of a fiber array reader 1800. Inthe case of very long fiber arrays 1814, the fiber array 1814 can berolled into a format similar to a typical audio-cassette tape. In thisconfiguration, one or more motors (not shown) move the array off one hub1818 and onto another hub 1820 with each fiber 110 passing under a fixeddetector optic 1826. Heater/cooler units 1824 may be provided in bothhubs 1818 and 1820. A laser 1870 is also provided. An ultrasonic mixingdevice 1804, which may be fixed in space, may be added to improve mixingof the fluids.

FIG. 19 is still another embodiment of a fiber array according to thepresent invention. The fiber array 1900 comprises a circular supportplate 1902 with the fibers 110 radially disposed on the support plate1902 such that one end of each fiber 110 is near the center of thesupport plate 1902 and the other end of the fiber 110 is near the outerperimeter of the support plate 1902. The fiber array 1900 also comprisesa plurality of channels 1904 in the support plate 1902. Although thechannels 1904 may be arranged in any fashion or pattern on the supportplate 1902, in some embodiments, the channels 1904 are arranged inconcentric circles; however, it should be appreciated that it is notnecessary to have a channel which traverses an entire concentric circle.For example, a channel 1904 may simply be the length of a portion of aconcentric circle or an arc. The light source 1906 and focusing lens1908 act to project and direct the beam of light 1910 to the end of eachof the fibers 110. In this embodiment, rather than move the light source1906 and the focusing lens 1908 to align the beam of light 1910 witheach fiber 110, the support plate 1902 is rotated such that each fiber110 is aligned with the beam of light 1910. Again, a motion detectionsystem (not shown) having motion sensors may be used to monitor theexact positioning of the support plate 1902 to provide exact alignmentwith the beam of light 1910. A cover 1912 may also be provided.

No image is necessary for the various readers, so a single diode maycollect the information. The signal from this diode can be quicklyconverted from analog to digital and recorded, reducing the amount ofdata as compared to a camera system. Since the detection system issimple and inexpensive, it is feasible to detect many channelssimultaneously, greatly increasing the throughput.

Furthermore, because the evanescence wave does not travel far beyond thefiber surface, the sample can remain in the channel duringhybridization, avoiding washing and allowing real-time reading. Thus,the fluorescent signal can be monitored while temperature is ramped.Rather than a snap-shot information, information on hybridization overtime is collected, providing much higher specificity and real timemonitoring.

The fiber arrays may contain 100,000 or more fibers that could bequickly detected by these readers and many channels may be readsimultaneously, resulting in a high density of information.

The light-source may also directly illuminate the mix points through thefiber to reduce stray light and unwanted reflections. Thus, reducing thenoise level. In a desirable contrast, the signal level is higher becausethe cylindrical shape of the fiber focuses fluorescence rays passingthrough it. This focusing results in the collection of fluorescence raysthat otherwise would be lost.

Furthermore, only the fibers are illuminated, avoiding the wastefulprocess of flood illuminating the entire surface area, and thus,reducing the amount of illumination power needed.

Any of the above reader embodiments may include an adaptive filter tofilter out common noise such as reflecting light. To calibrate thesystem all detectors are activated when no chemical species is present.All detectors are then set to zero using mathematical manipulation suchas a transfer function. The chemical species is then added to thesystem. Any change in signal from the detectors is therefore caused bythe added chemicals species.

In yet another aspect of the invention, the fibers 110, which have beendescribed above, are incorporated into a fiber wheel mixing system forcontacting at least two chemical species. It should be appreciated thatthe fiber wheel mixing system may be used for any of the chemicalinteractions described previously in connection with the fiber array.The fiber wheel mixing system generally includes a container forreceiving a mobile chemical species and a wheel including fibers havinga chemical species immobilized thereon. FIGS. 20 through 26 and 30 and31 show various embodiments of the fiber wheel mixing system. FIGS. 27to 29 show various embodiments of a light evaluating system fordetecting and evaluating light signals generated as a result of mixingbetween two chemical species.

FIG. 20 is a perspective view of a wheel 2000 having a plurality offibers 2011 each of which has a chemical species immobilized thereon.The wheel 2000 has a top 2002, a bottom 2003, a perimeter sidewall 2004,and a longitudinal axis (not shown) that runs through a center wheelaperture 2006 in a direction parallel to the fibers 201 1. Although thewheel 2000 may be shaped and sized to have any desired diameter andheight, it may be desired to have an aspect ratio greater than 1.0,where the aspect ratio is defined as a ratio of the wheel diameter tothe wheel height (i.e., the vertical distance between the top 2002 andthe bottom 2003 of the wheel 2000). The size of the wheel 2000 may beadjusted in order to accommodate the desired number of fibers 2011 to bedisposed thereon and the pre-determined spacing therebetween. Forexample, a wheel having a diameter of about 63 mm can accommodate on itssidewall up to 1,000 fibers (200 μm or less in diameter) whilemaintaining 200 μm of center-to-center distance between the adjacentfibers. The wheel diameter may range from 5 to 10 cm, although greateror less wheel diameters may be desired depending on the number of fibers2011 to be disposed and desirable spacing therebetween. The wheel 2000may also include the center wheel aperture 2006 for handling purposeswhich will be discussed in greater detail below.

Still referring to FIG. 20, a plurality of the fibers 2011 are disposedon the perimeter sidewall 2004 of the wheel 2000 via mechanical and/orchemical bonding. The fibers 2011 may be aligned parallel to each otherand in a direction parallel to the longitudinal axis of the wheel 2000.The fibers 2011 may also be arranged to maintain a uniform spacingtherebetween. The sidewall 2004 may include a plurality of grooves 2005,each of which extends from the top 2002 and terminates at the bottom2003 of the wheel 2000. The grooves 2005 are shaped and sized to receivethe fibers 2011 and to facilitate the alignment of the fibers 2011. Thegrooves 2005 may also be shaped to retain the fibers 2011. In addition,it should be appreciated that the grooves may being optically curvatiousto reflect the light into the detectors in a manner which promotesoptimum collection efficiency. It should be appreciated that anygeometic curvature of the grooves may be used to reflect light to thedetectors.

FIG. 21 is a perspective view of a cylinder 2100 having a plurality offibers 2011 each having immobilized thereon a chemical species. Thecylinder 2100 may have a length much greater than its diameter such thatthe fibers 2011 can be of any desired length along a surface 2103 of thecylinder 2100. For example, the fibers 2011 may be 5 tolO centimeters inlength on the surface 2103 of the cylinder 2100 which may have adiameter of about 63 mm. The cylinder 2100 may include a center cylinderaperture 2106 for ease of handling. Once disposed with the fibers 2011,the cylinder 2100 may be pre-cut and/or pre-perforated at pre-describedlengths in order to pre-form a plurality of wheels 2000 readilyseparable in a direction perpendicular to a longitudinal axis of thecylinder 2100. It should be appreciated that the cylinder may becomprised of separate wheels that are connected using a fastener, suchas a snap, or adhesive, such as glue or tape, so that after the fibersare placed on the cylinder, the wheel may be easily separated. The wheel2000 having a pre-described height can then be prepared by separating anend wheel unit 2000 from the rest of the cylinder 2100, for example, byapplying mechanical force, such as a knife or water jet, heat, such aslaser cutting, or by other separatiop methods known in the art. One ormore wheels 2000 can be separated from the cylinder 2100 with care takennot to contaminate the chemical species from one fiber onto another.Wheels 2000 and cylinders 2100 may be made of a materials similar tothat of the fiber array. The surface of the wheel 2000 and the cylinder2100 may also be provided with features such as low-fluorescence or areflective coating, for example, the cylinder may be made of plastichaving a vapor deposited gold coating.

FIG. 22 is a cross-sectional view of a wheel 2000 coupled to a wheelrotation device 2201 through a rotational coupler, such as an axle 2202positioned therebetween. By coupling one end of the axle 2202 to thewheel rotation device 2201 and by fixedly coupling the other end of theaxle 2202 to the wheel 2000 through its center wheel aperture 2006, thewheel 2000 can be rotated by the wheel rotation device 2201, such as anelectric motor, a manual rotation assembly, or other rotation devicesknown in the art. A sealing disk 2203 may be positioned between thewheel 2000 and the wheel rotation device 2201. The disk 2203 may beshaped and sized according to the dimension of the container such thatthe disk 2203 may serve as a cover plate that sealingly engages thecontainer, as will be described later. The disk 2203 is looselyconstrained by the axle 2202 which passes through a center disk aperture2204. A bottom surface of the disk 2203 may be shaped to be concavetoward the top 2002 of the wheel 2000 in order to minimize rotationalfriction therebetween. A lock washer 2205 may also be provided on top ofthe disk 2203 and arranged to lightly press both the wheel 2000 and thedisk 2203 downwardly. It should be appreciated that the axle 2202 isonly one example of the rotational coupler that may be used to couplethe wheel 2000 to the wheel rotation device 2201. For example, acylinder 2100 and a wheel 2000 may be fabricated without any centerapertures 2006, 2106 therein. One of skill in the art would recognizethat such wheels 2000 without center wheel aperture 2006 can be coupledto and rotated by the wheel rotation device 2201 using other rotationalcouplers such as a vacuum chuck, magnet, and other rotatable couplingelements known in the art.

FIG. 23 is a cross-sectional view of a container 2300 coupled to acontainer rotation device 2306. The container 2300 is capable ofreceiving and storing the mobile chemical species therein and receivingat least a portion of the perimeter sidewall 2004 of the wheel 2000. Thecontainer 2300 may be an open cylinder having a top opening 2301, acavity 2302, and container sidewalls 2305. The cavity 2302 is defined bya cavity sidewall 2303 and a cavity bottom surface 2304. Because thecontainer 2300 is to receive the wheel 2000 therein, the configurationof the container 2300 is determined by the shape and size of the wheel2000. In addition, the container 2300 is also arranged to form anannular chamber gap with pre-described dimensions between the cavitysidewall 2303 and the perimeter sidewall 2004 of the wheel 2000 (thechamber gap is shown in FIG. 25, i.e., an annular ring-shaped space thatupon rotation will be filled with the mobile chemical species 2310). Thechamber gap generally has a thickness less than a few centimeters andwithin the range of 0.5 to 1.5 mm. The cavity bottom surface 2304 may beshaped to be concave upward to minimize rotational friction against thebottom 2003 of the wheel 2000 and to displace the mobile chemicalspecies 2310 toward the cavity sidewall 2303. The container 2300 isgenerally made of a low cost inert material so that it can be disposedafter use. The container sidewall 2305 and/or cavity sidewall 2303 maybe made of flexible material similar to that of the fiber arrays. Itshould be appreciated that the container may generally be made ofmaterials the same as or similar to the fiber arrays.

Still referring to FIG. 23, the container 2300 is mechanically coupledto the container rotation device 2306 through a platform 2307 positionedtherebetween. A top surface of the platform2307 is shaped and sized toreceive the container 2300 such that the container rotation device 2306can rotate the platform 2307 along with the container 2300. The platform2307 may include a heating element 2311, a temperature sensor 2312 or atemperature controller 2313 for heating the fluid stored in thecontainer 2300 and controlling the temperature thereof.

FIG. 24 is a cross-sectional view of a fluid delivery system 2400according to the present invention. In general, a fluid pathway 2401 isembedded inside the wheel 2000 and terminates at one or more inlet ports2402 and outlet ports 2403. The mobile chemical species is loadedthrough the inlet port 2402, moves through the fluid pathway 2401 towardthe outlet port 2403, and is discharged into the chamber gap (shown inFIG. 25) formed between the cavity sidewall 2303 and the perimetersidewall 2004 of the wheel 2000. Gravity, capillary force, centrifugalforce, and/or electomotive force may be used as the driving force formoving the mobile chemical species through the fluid pathway 2401. Afilter (not shown) may be provided at the inlet and/or outlet ports2402, 2403, or along the fluid pathway 2401 in order to removeundesirable substances from the mobile chemical species. Filtration maybe accomplished by adsorption, absorption, filtration or other filteringmechanisms known in the art.

FIGS. 25 and 26 are a cross-sectional view and a top-plan view of afiber wheel mixing system 2500, respectively. In operation, the mobilechemical species 2310 is loaded into the cavity 2302 of the container2300 by the fluid delivery system 2400 described above (shown in FIG.31). Alternatively, the mobile chemical species 2310 may be directlyloaded into the container cavity 2302 with a syringe or pipette or byother manual or automated means. As illustrated in FIGS. 25 and 26, thefiber wheel mixing system 2500 is assembled by positioning the wheel2000 inside the container cavity 2302, by fitting the disk 2203 onto thetop opening 2301 of the container 2300, by sealingly engaging the disk2203 around the top opening 2301, and by forming a closed space forcontaining the mobile chemical species 2310. The wheel 2000 and thecontainer 2300 are rotated by the corresponding rotation devices 2201,2306. The speed and duration of the rotation may vary depending on thechemical reaction rates and may range from seconds to hours. The mobilechemical species 2310 is then displaced toward the cavity sidewall 2303by the centrifugal force, and forms an annular column of fluid 2310. Ingeneral, the thickness of the fluid column is determined by severalfactors such as the cavity diameter, cavity height, chamber gapdimension, and the amount of the mobile chemical species 2310 loadedinto the container cavity 2302. By filling the chamber gap with apre-described amount of the mobile chemical species 2310, the chemicalspecies immobilized on the fibers 2011 of the wheel 2000 can contact themobile chemical species 2310.

It is appreciated that the wheel 2000 and the container 2300 may becounter-rotated at a speed enough to generate a turbulent mixing zone atthe mix points. The turbulent mixing increases the contact efficiencyand minimizes the amount of the chemical species required for efficientmixing therebetween. Rotational speeds necessary to form the turbulentmixing zone can be easily determined and confirmed by introducing anindicator or dye into the mixing zone and observing the mixing patterntherein, or by analyzing the intensity of the light signals emanatingfrom the fibers 2011 which will be discussed in greater detail below.One of skill in the art would recognize that rotating only one of thewheel 2000 or the container 2300 can also generate a similar turbulentmixing zone.

Clearances 2501, 2502 may be provided at the contacting zones betweenthe disk 2203 and the wheel 2000, and between the wheel 2000 and thecavity bottom surface 2304. These clearances 2501, 2502 minimize therotational friction and may serve as an additional fluid channel throughwhich the mobile chemical species 2310 can be displaced during rotationfrom a cavity center toward the cavity sidewall 2303.

FIGS. 27 and 28 show two embodiments of a light evaluating system 2700for detecting light signals generated as a result of mixing two or morechemical species. The light evaluating system 2700 typically includes alight source 2701, light guiding devices 2702 a, 2702 b, and a lightdetecting device 2703. The light source 2701, such as a laser or an arclamp, produces a beam of light 2705 with the desired wavelength that isdirected to one end of the fiber 2711. Appropriate light source 2701 anddesired wavelength of the light can be selected by methods similar tothose described above in connection with the fiber array 100. Forpurposes of the present invention, the fibers 2011 are optical fibers,details of which have already been described above. The light source2701 is located under the platform 2307 such that the light beam 2705 isdirected to the end of the fiber 2011 and internally reflects therein.The reflected light beam 2705 creates an evanescent wave on a surface ofthe fiber 2011 illuminating the chemical species attached thereto.Because the intensity of the evanescent wave exponentially dissipateswith distance from the surface of the fiber 2011 (almost disappearingbeyond 300 nm), the chemical species is illuminated but not the materialsurrounding the fiber 2011, i.e., only the fiber 2011 fluoresces. Morespecifically and as described above, only those locations along eachfiber 2011 where some type of interaction between the chemical specieshas occurred will produce a detectable signal such as fluorescence. Thelight guiding device such as a focusing lens 2702 a and a reflectingmirror 2702 b may be used to collect photons generated by fluorescencefrom the fibers 2011 and to focus the photons into the light detectingdevice 2703. Examples of such light guiding devices include, but are notlimited to, lenses, mirrors, prisms, and other optical elements known inthe art. The light guiding device 2702 a, 2702 b as well as optionalreflective coating on the perimeter sidewall 2704 of the wheel 2000directs more photons into the light detecting device 2703, therebyimproving the signal-to-noise ratio of the detected light signals.

In operation, after measuring the light signal at a given mix point oralong a given fiber 2711, the wheel 2000 is sequentially rotated eithermanually or automatically. The rotation places a new mix point and/or anew fiber into the field of the light evaluating system 2700 and alignsthe light beam 2705 into an end of the new fiber. It is appreciated thatan optional light guiding device may be positioned between the lightsource 2701 and the platform 2307 to focus the light beam 2705 on theend of the fiber 2011. An optional motion device 2704 may be used tomove the light source 2701 and/or the light guiding devices 2702 a, 2702b along a perimeter of the wheel 2000 to properly align the light beam2705 with the end of each fiber 2011. In addition, an optional motiondetecting system with motion sensors (not shown), such as infrared lightsensors, may be used to monitor the position of the motion device 2704.

FIG. 29 shows another embodiment of a light evaluating system 2900. Thephotons collected into the light detecting device 2703 generate electriccurrent in proportion to the number of photons detected. This electricalsignal is amplified, processed, and plotted over time by an electricaldevice 2901, e.g., an oscilloscope or computer. As described above,after measuring the light signal at a given mix point or along a givenfiber 2011, the wheel 2000 is sequentially rotated and a new mix pointor a new fiber is brought into the field of the light evaluating system2900. The light beam 2705 is aligned into an end of the new fiber andthe above procedures are repeated.

FIGS. 30 and 31 illustrate another embodiment of a fiber wheel mixingsystem 3000 including a wheel assembly 3001 and a multi-cavity container3010. FIG. 30 is a cross-sectional view of the system 3000 along arotational coupler, such as a rotation axle 3002. FIG. 31 is across-sectional view of the system 3000 in a direction perpendicular tothe rotation axle 3002 of FIG. 30. The wheel assembly 3001 includesmultiple wheels 2000 vertically positioned along the rotation axle 3002through their center wheel apertures 2006, and is rotatably coupled tothe wheel rotation device 2201. The multi-cavity container 3010 consistsof a top portion 3011 and a bottom portion 3012, and each of top andbottom portions 3011, 3012 includes top and bottom dividers 3013, 3014,respectively. The top portion 3011 and top dividers 3013 are arranged tofit over the bottom portion 3012 and corresponding bottom dividers 3014such that multiple cavities 3015 form within the container 3010. Themulti-cavity container 3010 may also be rotatably coupled to thecontainer rotation device 2306.

In operation, the wheel assembly 3001 is assembled and positioned insidethe bottom portion 3012 of the multi-cavity container 3010 such thatabout a lower half of each wheel 2000 is received by a correspondingcavity 3015 of the bottom portion 3012. The top portion 3011 is thensealingly engaged over the bottom portion 3012, and each cavity 3015sealingly separates a corresponding wheel 2000 from its neighbors. Themobile chemical species 3010 is loaded into each cavity 3015 eitherdirectly with a syringe or pipette or through a fluid delivery systemsimilar to the one described in FIG. 24. At least one of the wheelassembly 3001 or the multi-cavity container 3010 is rotated by thecorresponding rotation devices 2201, 2306, thereby contacting the secondimmobilized chemical species with the mobile chemical species 3020stored in the cavities 3015. One skilled in the art would recognize thateach cavity 3015 may be loaded with different chemical species and thateach wheel 2000 may be disposed with fibers immobilized with differentchemical species. Because the processing time for multiple samples isnot much greater than that for processing a single sample, themulti-wheel-multi-chamber system of FIGS. 30 and 31 offers a benefit ofreducing labor cost per sample. It is appreciated that other featuresand advantages of the fiber wheel mixing system 2000 described in FIGS.20 through 27 equally apply to the multi-wheel-multi-chamber system 3000of FIGS. 30 and 31. For example, the wheel assembly 3001 and themulti-cavity container 3010 can be counter-rotated at a speed enough togenerate a turbulent mixing zone at the mix points.

In a further embodiment of the invention, instead of fibers, an array ofspots or dots of a chemical species may be incorporated into the wheelmixing system. These spots form a cylindrical micro-array on an outersurface of a wheel. The spots may be immobilized onto a distinctsubstrate which is capable of transmitting light, or directly onto theouter perimeter of the wheel itself, where the wheel is made of a lighttransmitting material. The chemical species immobilized onto thesubstrate may either be directly applied onto the wheel, onto thesubstrate positioned around the circumference of the wheel or onto aflat substrate which is later conformed to the shape of the wheel. Lightentering the light transmitting material from a laser, forms anevanescent wave close to the perimeter surface of the wheel which usingthe reader described above, is used to detect binding of the chemicalspecies. The light transmitting material may be a glass material.

The fiber wheel mixing apparatus provides a high-quality apparatus forcontacting different chemical species. Because the fibers can be easilytested to determine the quality of immobilization of the chemicalspecies on the fiber, high quality fibers may be selected for use on thewheel.

In addition, the fibers of the present invention are completely driedafter being immobilized with a chemical species and before beingdisposed on the wheel. Accordingly, contamination between mix points maybe prevented, since there is little possibility of splattering onechemical species onto another, as can be the case with robot spotting.

The fiber wheel mixing apparatus is also relatively easy to use. Thesample containing a mobile chemical species is simply loaded into thecontainer with a syringe or pipette or by an appropriate fluid deliveryapparatus. The wheel is placed into the container and a rotation deviceis activated. In case post-mixing washing should be necessary, the wheelcan be removed from the container and dipped into a washing solution.Signals generated as a result of mixing can be detected and evaluated ina number of ways. The container can be discarded after use, thuseliminating the need for washing containers and reducing the potentialfor contamination.

Furthermore, by rotating both the wheel and the container in oppositedirections, the fiber wheel mixing apparatus creates a turbulent mixingzone around the mix points. The turbulent mixing dramatically increasesthe contact efficiency. Due to such a highly efficient mixing mechanism,only a minimum amount of the second immobilized chemical species isrequired for mixing and analysis, which is far less than that of moreconventional approaches.

The fiber wheel mixing apparatus also significantly improves thesignal-to-noise ratio of the signals. For example, the light detectingdevice can analyze the light signals directly emanating from the mixpoints. With little stray to cause undesirable reflections, the noisecollected by the light detecting device should be very low. In adesirable contrast, the amount of photons collected into the lightdetecting device is high because the wheel geometry, lenses, mirrors,and reflectors focus very high percentages of the light signal into thelight detecting device. The high signal-to-noise ratio also providessignificant improvement in the dynamic range and sensitivity of thefiber wheel mixing apparatus by two orders of magnitude over typicalconventional spotting techniques.

Those of skill in the art will recognize that the fiber arrays of theinvention can be used in virtually any assay where detectinginteractions between to chemical species is desired. For example, thefiber arrays can be conveniently used to screen for and identifycompounds which bind a receptor of interest, such as peptides which bindan antibody, organic compounds which bind an enzyme or receptor orcomplementary polynucleotides which bind (hybridize to) one another.However, the arrays of the invention are not limited to applications inwhich one chemical species binds another. The arrays of the inventioncan also be used to screen for and identify compounds which catalyzechemical reactions, such as antibodies capable of catalyzing certainreactions, and to screen for and identify compounds which give rise todetectable biological signals, such as compounds which agonize areceptor of interest. The only requirement is that the interactionbetween the two chemical species give rise to a detectable signal. Thus,the fiber arrays of the invention are useful in any applications thattake advantage of arrays or libraries of immobilized compounds, such asthe myriad solid-phase combinatorial library assay methodologiesdescribed in the art. For a brief review of the various assays for whichthe fiber arrays of the invention can be readily adapted, see Gallop etal., 1994, J. Med. Chem. 37:1233-1251; Gordon et al., 1994, J. Med.Chem. 37:1385-1401; Jung, 1992, Agnew Chem. Pat. Ed. 31:367-386;Thompson & Ellman, 1996, Chem Rev. 96: 555-600, and the references citedin all of the above.

The fiber arrays of the invention are particularly useful forapplications involving hybridization of nucleic acids, especially thoseapplications involving high density arrays of immobilizedpolynucleotides, including, for example, de novo sequencing byhybridization (SBH) and detection of polymorphisms. In theseapplications, conventional immobilized polynucleotide arrays typicallyused in the art can be conveniently and advantageously replaced with thefiber arrays of the invention. For a review of the various array-basedhybridization assays in which the fiber arrays of the invention finduse, see U.S. Pat. No. 5,202,231; U.S. Pat. No. 5,525,464; WO 98/31836,and the references cited in all of the above.

Based on the above, those of skill in the art will recognize that thechemical species immobilized on the fiber can be virtually any types ofcompounds, ranging from organic compounds such as potential drugcandidates, polymers and small molecule inhibitors, agonists and/orantagonists, to biological compounds such as polypeptides,polynucleotides, polycarbohydrates, lectins, proteins, enzymes,antibodies, receptors, nucleic acids, etc. The only requirement is thatthe chemical species be capable of being immobilized on the fiber.

In a some embodiments, the chemical species immobilized on the fiber isa polynucleotide. Typically, the polynucleotide will be of astrandedness and length suitable for format II and format III SBH andrelated applications. Thus, the polynucleotide will generally besingle-stranded and be composed of between about 4 to 30, typicallyabout 4 to 20, and usually about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or20 nucleotides. However, it will be recognized that the fiber arrays ofthe invention are equally well suited for use with format I SBH, andrelated applications, where an immobilized target nucleic acid isinterrogated with solution-phase oligonucleotide probes. Thus, thepolynucleotide can be any number of nucleotides in length and be eithersingle- or double-stranded, depending on the particular application.

The polynucleotide may be composed entirely of deoxyribonucleotides,entirely of ribonucleotides, or may be composed of mixtures of deoxy-and ribonucleotides. However, due to their stability to RNases and hightemperatures, as well as their ease of synthesis, polynucleotidescomposed entirely of deoxyribonucleotides may be preferred.

The polynucleotide may be composed of all natural or all syntheticnucleotide bases, or a combination of both. While in most instances thepolynucleotide will be composed entirely of the natural bases (A, C, G,T or U), in certain circumstances the use of synthetic bases may bepreferred. Common synthetic bases of which the polynucleotide may becomposed include 3-methlyuracil, 5,6-dihydrouracil, 4-thiouracil,5-bromouracil, 5-thorouracil, 5-iodouracil, 6-dimethyl amino purine,6-methyl amino purine, 2-amino purine, 2,6-diamino purine,6-amino-8-bromo purine, inosine, 5-methyl cytosine, and 7-deazaquanosine. Additional non-limiting examples of synthetic bases of whichthe polynucleotide can be composed can be found in Fasman, CRC PracticalHandbook of Biochemistry and Molecular Biology, 1985, pp. 385-392.

Moreover, while the backbone of the polynucleotide will typically becomposed entirely of “native” phosphodiester linkages, it may containone or more modified linkages, such as one or more phosphorothioate,phosphoramidite or other modified linkages. As a specific example, thepolynucleotide may be a peptide nucleic acid (PNA), which contains amideinterlinkages. Additional examples of modified bases and backbones thatcan be used in conjunction with the invention, as well as methods fortheir synthesis can be found, for example, in Uhlman & Peyman, 1990,Chemical Review 90(4):544-584; Goodchild, 1990, Bioconjugate Chem.1(3):165-186; Egholm et al., 1992, J. Am. Chem. Soc. 114:1895-1897;Gryaznov et al., J. Am. Chem. Soc. 116:3143-3144, as well as thereferences cited in all of the above.

While the polynucleotide will often be a contiguous stretch ofnucleotides, it need not be. Stretches of nucleotides can be interruptedby one or more linker molecules that do not participate insequence-specific base pairing interactions with a target nucleic acid.The linker molecules may be flexible, semi-rigid or rigid, depending onthe desired application. A variety of linker molecules useful forspacing one molecule from another or from a solid surface have beendescribed in the art (and have been described more thoroughly supra);all of these linker molecules can be used to space regions of thepolynucleotide from one another. In a some embodiments of this aspect ofthe invention, the linker moiety is from one to ten, more specificallytwo to six, alkylene glycol moieties, such as ethylene glycol moieties.

The polynucleotide can be isolated from biological samples, generated byPCR reactions or other template-specific reactions, or madesynthetically. Methods for isolating polynucleotides from biologicalsamples and/or PCR reactions are well-known in the art, as are methodsfor synthesizing and purifying synthetic polynucleotides.Polynucleotides isolated from biological samples and/or PCR reactionsmay, depending on the desired mode of immobilization, requiremodification at the 3′- or 5′-terminus, or at one or more bases, as willbe discussed more thoroughly below. Moreover, since the polynucleotidemust typically be capable of hybridizing to another target nucleic acid,if not already single stranded, it may be rendered single stranded,either before or after immobilization on the fiber.

Depending on the identity of the chemical species and the fibermaterial, the chemical species can be immobilized by virtually any meansknown to be effective for immobilizing the particular type of chemicalspecies on the particular type of fiber material. For example, thechemical species can be immobilized via absorption, adsorption, ionicattraction or covalent attachment. The immobilization may also bemediated by way of pairs of specific binding molecules, such as biotinand avidin or streptavidin. Methods for immobilizing a variety ofchemical species to a variety of materials are known in the art. Any ofthese art-known methods can be used in conjunction with the invention.

For adsorption or absorption, fiber 11 can be conveniently prepared bycontacting the fiber with the chemical species to be immobilized for atime period sufficient for the chemical species to adsorb or absorb ontothe fiber. Following optional wash steps, the fiber is then dried. Whenthe chemical species is a polynucleotide, the various methods describedin the dot-blot or other nucleic acid blotting arts for immobilizingnucleic acids onto nitrocellulose or nylon filters can be convenientlyadapted for use in the present invention.

For immobilization by ionic attraction, if not inherently charged, thefiber is first activated or derivatized with charged groups prior tocontacting it with the chemical species to be immobilized, which iseither inherently oppositely charged or has been modified to beoppositely charged.

For immobilization mediated by way of specific binding pairs, the fiberis first derivatized and/or coated with one member of the specificbinding pair, such as avidin or streptavidin, and the derivatized fiberis then contacted with a chemical species which is linked to the othermember of the specific binding pair, such as biotin. Methods forderivatizing or coating a variety of materials with binding moleculessuch as avidin or streptavidin, as well as methods for linking myriadtypes of chemical species to binding molecules such as biotin are wellknown in the art. For polynucleotide chemical species, biotin can beconveniently incorporated into the polynucleotide at either a terminaland/or internal base, or at one or both of its 5′- and 3′- termini usingcommercially available chemical synthesis or biological synthesisreagents.

In a some embodiments of the invention, the chemical species iscovalently attached to the fiber, optionally be way of one or morelinking moieties. Unless the fiber inherently contains reactivefunctional groups capable of forming a covalent linkage with thechemical species, it must first be activated or derivatized with suchreactive groups. Typical reactive groups useful for effecting covalentattachment of chemical species to the fiber include hydroxyl, sulfonyl,amino, cyanate, isocyanate, thiocyanate, isothiocyanate, epoxy andcarboxyl groups, although other reactive groups as will be apparent tothose of skill in the art may also be used.

A variety of techniques for activating myriad types of fiber materialswith reactive groups suitable for covalently attaching chemical speciesthereto, particularly biological molecules such as polypeptides,proteins, polynucleotides and nucleic acids, are known in the art andinclude, for example, chemical activation, corona discharge activation;flame treatment activation; gas plasma activation and plasma enhancedchemical vapor deposition. Any of these techniques can be used toactivate the fiber with reactive groups. For a review of the manytechniques that can be used to activate or derivatize the fiber, seeWiley Encyclopedia of Packaging Technology, 2d Ed., Brody & Marsh, Ed.,“Surface Treatment,” pp. 867-874, John Wiley & Sons, 1997, and thereferences cited therein. Chemical methods suitable for generating aminogroups on glass optical fibers are described in Atkinson & Smith, “SolidPhase Synthesis of Oligodeoxyribonucleotides by the Phosphite TriesterMethod,” In: Oligonucleotide Synthesis: A Practical Approach, M J Gait,Ed., 1985, IRL Press, Oxford, particularly at pp. 45-49 (and thereferences cited therein); chemical methods suitable for generatinghydroxyl groups on optical glass fibers are described in Pease et al.,1994, Proc. Natl. Acad. Sci. USA 91:5022-5026 (and the references citedtherein); chemical methods suitable for generating functional groups onfiber materials such as polystyrene, polyamides and grafted polystyrenesare described in Lloyd-Williams et al., 1997, Chemical Approaches to theSynthesis of Peptides and Proteins, Chapter 2, CRC Press, Boca Raton,Fla. (and the references cited therein). Additional methods arewell-known, and will be apparent to those of skill in the art.

For fibers coated with a conductor, such as gold, the chemical speciescan be attached to the conductor using known chemistries. For example, apolynucleotide can be covalently attached to a gold-coated fiber usingthe methods described in Heme & Taylor, 1997, J. Am. Chem. Soc.119:8916-8920. This chemistry can be readily adapted for covalentlyimmobilizing other types of chemical species onto a gold-coated fiber.

Depending on the nature of the chemical species, it can be covalentlyimmobilized on the activated fiber following synthesis and/or isolation,or, where suitable chemistries are known, it may be synthesized in situdirectly on the activated fiber. For example, a purified polypeptide maybe covalently immobilized on an amino-activated fiber, conveniently byway of its carboxy terminus or a carboxyl-containing side chain residue.Alternatively, the polypeptide can be synthesized in situ directly on anamino-activated fiber using conventional solid-phase peptide chemistriesand reagents (see Chemical Approaches to the Synthesis of Peptides andProteins, Lloyd-Williams et al., Eds., CRC Press, Boca Raton, Fla., 1997and the references cited therein). Similarly, a purified polynucleotidebearing an appropriate reactive group at one or more of its bases ortermini can be covalently immobilized on an isothiocyanate- orcarboxy-activated fiber, or alternatively, the polynucleotide can besynthesized in situ directly on a hydroxyl-activated fiber usingconventional oligonucleotide synthesis chemistries and reagents (seeOligonucleotide Synthesis: A Practical Approach, 1985, supra, and thereferences cited therein). Other types of compounds which can beconveniently synthesized by solid phase methods can also be synthesizedin situ directly on a fiber. Non-limiting examples of compounds whichcan be synthesized in situ include Bassenisi and Ugi condensationproducts (WO 95/02566), peptoids (Simon et al., 1992, Proc. Natl. Acad.Sci. USA 89:9367-9371), non-peptide non-oligomeric compounds (Dewitt etal., 1993, Proc. Natl. Acad. Sci. USA 90:6909-6913) and 1,4benzodiazepines and derivatives (Bunin et al., 1994, Proc. Natl. Acad.Sci. USA 91:4708-4712); Bunin & Ellman, 1992, J. Am. Chem. Soc.114:10997-10998).

Those of skill in the art will recognize that when using in situchemical synthesis, the covalent bond formed between the immobilizedchemical species and the fiber must be substantially stable to thesynthesis and deprotection conditions so as to avoid loss of thechemical species during synthesis and/or deprotection. Forpolynucleotides, one such stable bond is the phosphodiester bond, whichconnects the various nucleotides in a polynucleotide, and which can beconveniently formed using well-known chemistries (see, e.g.,Oligonucleotide Synthesis: A Practical Approach, 1985, supra). Otherstable bonds suitable for use with hydroxyl-activated fibers includephosphorothiate, phosphoramidite, or other modified nucleic acidinterlinkages. For fibers activated with amino groups, the bond could bea phosphoramidate, amide or peptide bond. For fibers activated withepoxy functional groups, a stable C-N bond could be formed. Suitablereagents and conditions for forming such stable bonds are well known inthe art.

In one particularly convenient embodiment, a polynucleotide isimmobilized on a fiber by in situ synthesis on a hydroxyl-activatedfiber using commercially available phosphoramidite synthesis reagentsand standard oligonucleotide synthesis chemistries. In this mode, thepolynucleotide is covalently attached to the activated fiber by way of aphosphodiester linkage. The density of polynucleotide covalentlyimmobilized on the filter can be conveniently controlled by adding anamount of the first synthon (e.g., N-protected5′-O-dimethoxytrityl-2′-deoxyribonucleotide-3′-O-phosphoramidite)sufficient to provide the desired number of synthesis groups on thefiber, and capping any unreacted hydroxyl groups on the fiber with acapping reagent (e.g., 1,4-diaminopyridine; DMAP). After the excesshydroxyls have been capped, the trityl group protecting the 5′-hydroxylcan be removed and synthesis of the polynucleotide carried out usingstandard techniques. Following synthesis, the polynucleotide isdeprotected using conventional methods.

In an alternative embodiment, a polynucleotide is covalently attached tothe activated fiber through a post-synthesis or post-isolationconjugation reaction. In this embodiment, a pre-synthesized or isolatedpolynucleotide which is modified at its 3′-terminus, 5-terminus and/orat one of its bases with a reactive functional group (e.g. epoxy,sulfonyl, amino or carboxyl) is conjugated to an activated fiber via acondensation reaction, thereby forming a covalent linkage. Again,substantially stabile (i.e., non-labile) covalent linkages such asamide, phosphodiester and phosphoramidate linkages may be preferred.Synthesis supports and synthesis reagents useful for modifying the 3′-and/or 5′-terminus of synthetic polynucleotides, or for incorporating abase modified with a reactive group into a synthetic polynucleotide, arewell-known in the art and are even commercially available.

For example, methods for synthesizing 5′-modified oligonucleotides aredescribed in Agarwal et al., 1986, Nucl. Acids Res. 14:6227-6245 andConnelly, 1987, Nucl. Acids Res. 15:3131-3139. Commercially availableproducts for synthesizing 5′-amino modified oligonucleotides include theN-TFA-C6-AminoModiferm, N-MMT-C6-AminoModifer™ andN-MMT-C12-AminoModifier™ reagents available from Clontech Laboratories,Inc., Palo Alto, Calif.

Methods for synthesizing 3′-modified oligonucleotides are described inNelson et al., 1989, Nucl. Acids Res. 17:7179-7186 and Nelson et al.,1989, Nucl. Acids Res. 17:7187-7194. Commercial products forsynthesizing 3′-modified oligonucleotides include the 3′-Amino-ON™controlled pore glass and Amino Modifier II™ reagents available fromClontech Laboratories, Inc., Palo Alto, Calif.

Other methods for modifying the 3′ and/or 5′ termini ofoligonucleotides, as well as for synthesizing oligonucleotidescontaining appropriately modified bases are provided in Goodchild, 1990,Bioconjugate Chem. 1:165-186, and the references cited therein.Chemistries for attaching such modified oligonucleotides to materialsactivated with appropriate reactive groups are well-known in the art(see, e.g., Ghosh & Musso, 1987, Nucl. Acids Res. 15:5353-5372; Lund etal., 1988, Nucl. Acids Res. 16:10861-10880; Rasmussen et al., 1991,Anal. Chem. 198:138-142; Kato & Ikada, 1996, Biotechnology andBioengineering 51:581-590; Timofeev et al., 1996, Nucl. Acids Res.24:3142-3148; O'Donnell et al., 1997, Anal. Chem. 69:2438-2443).

Methods and reagents for modifying the ends of polynucleotides isolatedfrom biological samples and/or for incorporating bases modified withreactive groups into nascent polynucleotides are also well-known andcommercially available. For example, an isolated polynucleotide can bephosphorylated at its 5′-terminus with phosphorokinase and thisphosphorylated polynucleotide covalently attached onto anamino-activated fiber through a phosphoramidate or phosphodiesterlinkage. Other methods will be apparent to those of skill in the art.

In one convenient embodiment of the invention, a polynucleotide modifiedat its 3′- or 5′-terminus with a primary amino group is conjugated to acarboxy-activated fiber. Chemistries suitable for forming carboxamidelinkages between carboxyl and amino functional groups are well-known inthe art of peptide chemistry (see, e.g., Atherton & Sheppard, SolidPhase Peptide Synthesis, 1989, IRL Press, Oxford, England andLloyd-Williams et al., Chemical Approaches to the Synthesis of Peptidesand Proteins, 1997, CRC Press, Boca Raton, Fla. and the references citedtherein). Any of these methods can be used to conjugate anamino-modified polynucleotide to a carboxy-activated fiber.

In one embodiment, the carboxamide linkage is generated usingN,N,N′,N′-tetramethyl (succinimido) uronium tetrafluoroborate (“TSTU”)as a coupling reagent. Reaction conditions for the formation ofcarboxyamides with TSTU that can be used in conjunction with nucleicacids are described in Knorr et al., 1989, Tet. Lett. 30(15):1927-1930;Bannworth & Knorr, 1991, Tet. Lett. 32(9):1157-1160; and Wilchek et al.,1994, Bioconjugate Chem. 5(5):491-492.

Whether synthesized directly on the activated fiber or immobilized onthe activated fiber post-synthesis or post-isolation, the chemicalspecies can optionally be spaced away from the porous substrate by wayof one or more linkers. As will be appreciated by those having skill inthe art, such linkers will be at least bifunctional, i.e., they willhave one functional group or moiety capable of forming a linkage withthe activated fiber and another functional group or moiety capable offorming a linkage with another linker molecule or the chemical species.The linkers may be long or short, flexible or rigid, charged oruncharged, hydrophobic or hydrophilic, depending on the particularapplication.

In certain circumstances, such linkers can be used to “convert” onefunctional group into another. For example, an amino-activated fiber canbe converted into a hydroxyl-activated fiber by reaction with, forexample, 3-hydroxy-propionic acid. In this way, fiber materials whichcannot be readily activated with a specified reactive functional groupcan be conveniently converted into a an appropriately activated fiber.Chemistries and reagents suitable for “converting” such reactive groupsare well-known, and will be apparent to those having skill in the art.

Linkers can also be used, where necessary, to increase or “amplify” thenumber of reactive groups on the activated fiber. For this embodiment,the linker will have three or more functional groups. Followingattachment to the activated fiber by way of one of the functionalgroups, the remaining two or more groups are available for attachment ofthe chemical species. Amplifying the number of functional groups on theactivated fiber in this manner is particularly convenient when theactivated fiber contains relatively few reactive groups.

Reagents for amplifying the number of reactive groups are well-known andwill be apparent to those of skill in the art. A particularly convenientclass of amplifying reagents are the multifunctional epoxides sold underthe trade name DENACOL™ (Nagassi Kasei Kogyo K. K.). These epoxidescontain as many as four, five, or even more epoxy groups, and can beused to amplify fibers activated with reactive groups that react withepoxides, including, for example, hydroxyl, amino and sulfonyl activatedfibers. The resulting epoxy-activated fibers can be convenientlyconverted to a hydroxyl-activated fiber, a carboxy-activated fiber, orother activated fiber by well-known methods.

Linkers suitable for spacing biological or other molecules, includingpolypeptides and polynucleotides, from solid surfaces are well-known inthe art, and include, by way of example and not limitation, polypeptidessuch as polyproline or polyalanine, saturated or unsaturatedbifunctional hydrocarbons such as 1-amino-hexanoic acid and polymerssuch as polyethylene glycol, etc. For polynucleotide chemical species,one linker is polyethylene glycol (MW 100 to 1000).1,4-Dimethoxytrityl-polyethylene glycol phosphoramidites useful forforming phosphodiester linkages with hydroxyl groups ofhydroxyl-activated fibers, as well as methods for their use in nucleicacid synthesis on solid substrates, are described, for example in Zhanget al., 1991, Nucl. Acids Res. 19:3929-3933 and Durand et al., 1990,Nucl. Acids Res. 18:6353-6359. Other methods of attaching polyethyleneglycol linkers to activated fibers will be apparent to those of skill inthe art.

Regardless of the mode of immobilization, fibers 11 can be prepared in abatch-wise fashion where lengths of fiber are immersed in the solutionsnecessary to effect immobilization of the chemical species.Alternatively, fibers 11 can be prepared in a flow-through method inwhich the fiber is continuously flowed through reservoirs containing thesolutions necessary to effect immobilization.

FIG. 32 is one embodiment for preparation of the fiber for use in thefiber array according to the present invention in a batch-wise fashion.The fibers 3202 are attached to a fiber holder 3204 comprising fibergrippers 3206 which hold the fiber 3202. The fiber holder 3204 permitsthe fiber to be easily supported and transported and can be attached toany mechanical device (not shown) to automatically transport the fibers3202. A dipping vessel 3208 is a vessel that can contains a fluid to becontacted with the fibers 3202. In operation, the fibers 3202 areattached to the fiber grippers 3206, and the fiber holder 3204 lowersthe fibers 3202 into a solution contained in the dipping vessel 3208.The fiber holder 3204 then removes the fibers 3202 from the dippingvessel 3208. It should be appreciated that the fibers may besequentially placed into different dipping vessels each containingdifferent solutions depending upon the chemical species to beimmobilized on the fibers and the method used for immobilization. Afterthe chemical species has been immobilized on the fibers, the fibers maybe loaded onto a support plate or stored for future use. If the fibersare stored, refrigeration may be necessary depending upon the chemicalspecies on the fibers.

It is projected that with the present invention, once the fibers havebeen prepared as described, 100 fibers, each 10 cm in length, could belaid per second on a 10 cm support plate thereby producing 1,000,000contact points. It should be appreciated that laying the fibers on thesupport plate only requires accurate placement in a direction parallelto the channels to insure the fiber rests in the grooves on the channelwalls. Since the fiber can be placed anywhere in the direction parallelto the fiber, placing the fiber on the support plate is relativelysimple.

FIG. 33 is a process flow diagram of another embodiment for preparationof the fiber in a flow-through method for use in the fiber arrayaccording to the present invention. A motor 3301 is used to pull a fiber3304 from a fiber spool 3302 containing a length of material desired tobe used for the fibers 3304. If it is desired to coat the fiber 3304with a conductive coating, the fiber 3304 is first pulled through aconductive coating vat 3306 which contains a pool of conductive materialto be coated on the fiber 3304. More specifically, the conductivecoating vat 3306 utilizes meniscus coating to apply the conductivecoating to the fiber 3304, wherein the fiber 3304 is pulled through anarrow opening 3307 which only permits a thin layer of metal coating tobe applied to the fiber 3304. It should be appreciated that a conductivecoating is not required for use of the fiber array of the presentinvention. However, to utilize electro-osmosis, a metal or electricallyconductive oxide coating may be desired.

The fiber 3304 is then passed through a series of coating vats 3308,3310 depending upon the chemical species to be immobilized on the fibersand the method used for immobilization. Each coating vat may contain adifferent solution required to prepare the fiber and immobilize a givenchemical species on the fiber.

Lastly, the fiber 3304 is fed past the motor 3301 and is cut intodesired lengths by cutting apparatus 3312. It should be appreciated thatany length of fiber may be generated depending upon the size of thefiber array matrix. The cutting apparatus 3312 may be a laser or othermeans known in the art for cutting fibers or optical fibers. It shouldbe appreciated that it is important to obtain a very clean and straightcut if the fiber 3304 is an optical fiber so that in use the beam oflight directed at the end of the fiber is able to enter the fiber at thecorrect angle. Once cut, the fibers 1404 may be loaded onto a supportplate or stored for later use. If the fibers are stored, refrigerationmay be necessary depending upon the materials deposited on the fibers.

Following preparation by either of the methods described above, a lengthof fiber can be conveniently analyzed to verify the quality of theimmobilization process. For example, the chemical species immobilized ona portion of the fiber can be removed using conventional means andanalyzed using any of a variety of analytical techniques, including, forexample, gel electrophoresis (for polypeptides and polynucleotides),nuclear magnetic resonance, column chromatography, mass spectroscopy,gas chromatography, etc. Of course, the actual analytical means used toanalyze the fiber will depend on the nature of the chemical speciesattached thereto, and will be apparent to those of skill in the art.

In some embodiments, fibers 110 may also be prepared, i.e., the chemicalspecies may be immobilized to the fibers, while the fibers are disposedwithin the fiber array. In this embodiment, once the fibers are disposedin the support plate, the various fluids necessary to activate and/orimmobilize the chemical species to the fiber are flowed into channels108 to contact the fiber. This method is particularly convenient when itis desirable to immobilize different chemical species at differentspatial addresses along the length of the fiber.

The present invention is further directed to an apparatus and method forsynthesizing a chemical compound on a fiber. The synthesized fibers arethen used to fabricate fiber arrays discussed supra. This apparatus is afiber array multiplicative synthesizer that implements a direct processof moving a fiber through a plurality of coating modules that synthesizeone base onto the fiber. The coating modules can be stacked into columnswith a fiber passing out of one module into the next module. Each modulesequentially adds one base to the oligo. In one configuration, manycolumns of coating modules can be grouped into hubs, and those hubs canbe rotated relative to each other such that the number of differentoligos generated is much greater than the number of coating modulesdeployed, thus the name multiplicative synthesis. The fibers extractedfrom the multiplicative synthesizer system are directly loaded into afiber array. After sealing, the fiber array is immediately ready as ananalysis tool. In a second configuration, the modules are programmableto provide complex oligo configurations on-demand.

FIG. 34 is a diagrammatic drawing of a multiplicative fiber arraysynthesizer 3420 according to the present invention. The fiber arraysynthesizer 3420 comprises at least one, but often a plurality of,depositors 3422 where each of the depositors 3422 is capable ofdepositing a chemical species on a fiber 3426. The depositors 3422, asexplained in further detail below, may comprise a plurality of baths,spray chambers, wicking mechanisms, or the like. The multiplicativefiber array synthesizer 3420 further comprises a transporter 3424. Thetransporter 3424 may bring the fiber 3426 and the depositors 3422 intoproximity with one another, as indicated by control lines 3430, in orderto deposit at least one chemical species precursor on the fiber 3426 toform the chemical species. The transporter 3424 may move the depositors3422 into proximity with the fiber 3426, the fiber 3426 into proximitywith the depositors 3422, or both the depositors 3422 and the fiber 3426relative to one another. Alternatively, the transporter may comprise afluid delivery system for delivering the chemical species precursors toeach of said depositors 3422 the control of which is again indicated bythe control lines 3430. Specific examples of the transporter 3424 willbe discussed in further detail below. A selector 3428 controls the orderin which each of the at least one chemical species precursor isdeposited on the fiber 3426 from each of the depositors 3422. This maybe done by controlling the transporter 3424 to move the depositors 3422into proximity with the fiber 3426 in a predetermined order or bycontrolling the transporter 3424 to move the fiber 3426 into proximitywith the depositors 3422 in a predetermined order. The selector 3428 mayalso control the order in which each of the at least one chemicalspecies precursor is supplied to each of the depositors 3422 by thefluid delivery system.

FIG. 35A is a side view of one embodiment of depositors 3422 shown inFIG. 34. In this embodiment, each of the depositors 3422 comprise of atleast one bath 3532 containing a chemical species precursor 3536. Thechemical species precursor 3536 may for example comprise of a solutioncontaining phosphoramodites or other solutions such as washing solvents.In some embodiments, the transporter 3424 of FIG. 34 comprises a dippingmechanism for positioning the fiber 3526 in the bath 3532. The dippingmechanism may comprise a conveyor system such as a series of rollers3538 and 340 which frictionally engage with the fiber 3526 to push thefiber 3526 through the bath 3532 and hence into contact with thechemical species 3536. The dipping mechanism may alternatively comprisea mechanism for dipping substantially straight lengths, or coils of thefiber 3526 directly into the bath 3532 and the chemical species 3536.The fiber 3526 may be wound multiple times around an immersed roller3540 to vary the resonance time of the fiber 3526, as the fiber 3526 ismoved through the bath 3532 at a constant speed. This means that themore times the fiber 3526 is wound around the roller 3540, the longerthe fiber 3526 is exposed to the chemical species 3536. The roller 3540may comprise of a cage like device which allows all points along thefiber 3526 at some time or another, to be exposed to the chemicalspecies 3536.

FIG. 35B is a perspective view of another embodiment of the invention.In this embodiment, the transporter 3424 of FIG. 34 comprises a bathtransporter 3542 for moving the bath 3532, such that the chemicalspecies precursor 3536 is brought into contact with the fiber 3526.

FIG. 35C is a side view of yet another embodiment of the invention. Inthis embodiment, the transporter 3424 of FIG. 34 comprises a fluiddelivery system 3544 which delivers different chemical speciesprecursors or solutions into 3530 and out of 3548 the bath 3532.

FIG. 36A is a side view of an embodiment of depositors 3422 shown inFIG. 34. In this embodiment, each of the depositors 3422 comprise of atleast one spray chamber 3654 and a spray mechanism 3644 for spraying thechemical species precursor 3646 onto the fiber 3526. Again the chemicalspecies precursor 3646 may for example comprise of a solution containingphosphoramodites or other solutions such as washing solvents. In oneembodiment, the transporter 3424 of FIG. 34 comprises a fibertransportation mechanism such as a conveyor system 3656 whichfrictionally engages with the fiber 3526 to push the fiber 3526 throughthe spray chamber 3654.

FIG. 36B is a side view of another embodiment of depositors 3422 shownin FIG. 34. The transporter 3424 of FIG. 34 may alternatively compriseof a spray chamber transporter 3650 for bringing the spray chamber 3654into proximity with the fiber 3526.

FIG. 36C is a side view of yet another embodiment of depositors 3422shown in FIG. 34. In this embodiment, the transporter 3424 of FIG. 34comprises a fluid delivery system 3658 which delivers 3660 differentchemical species precursors or solutions to the spray mechanism 3644.

FIG. 37A is a side view of an embodiment of depositors 3422 shown inFIG. 34. In this embodiment, each of the depositors 3422 comprise of atleast one wicking mechanism 3762 for wicking a chemical speciesprecursor 3764 onto the fiber 3526. Yet again the chemical speciesprecursors may for example comprise of a solution containingphosphoramodites or other solutions such as washing solvents. Thetransporter 3424 of FIG. 34 comprises a fiber transportation mechanismsuch as a conveyor system 3766 which frictionally engages with the fiber3526.

FIG. 37B is a side view of another embodiment of depositors 3422 shownin FIG. 34. The transporter 3424 of FIG. 34 comprises a wickingmechanism transporter 3760 for bringing the wicking mechanism 3762 intoproximity with the fiber 3526.

FIG. 37C is a side view of another embodiment of depositors 3422 shownin FIG. 34. The transporter 3524 of FIG. 34 comprises a fluid deliverysystem 3770 which delivers different chemical species or solutions tothe wicking mechanism 3762.

In each of the above embodiments shown in FIGS. 35A to 37C, a mechanismto vary the resonance time of the fiber 3526 may be provided. Theselector 3428 of FIG. 34 may controls the transporter, in all of it'salternative embodiments, to vary the order in which each of theplurality of chemical species precursors are deposited on the fiber3526.

FIG. 38 is a perspective view of an embodiment of the invention, namelya fiber array multiplicative synthesizer 3802. Multiple spools 3804containing reeled-up fiber 3806 are mounted on a rotary platform 3808.The fibers 3806 typically comprise a flexible thread like material, suchas for example plastic or glass, and are wrapped around spools 3804 suchthat many meters can be stored but readily retrieved. The spools 3804are equally spaced in a circular pattern about the platform 3808 withthe fibers 3806 passing through the platform 3808. The platform 3808 isfixed to motor 3810, and the motor 3810 is fixed to a support shaft 3812that passes through the centers of the platform 3808 and both hubs 3814,3818. Motor 3816 is also fixed to the support shaft 3812. The platform3808 is rotatable about the support shaft 3812. The platform 3808 may berotated by a first rotation means 3810, such as a motor or the like. Anupper hub 3814 is also rotatable about the support shaft 3812 and may berotated by a second rotation means 3816 , such as a motor or the like. Alower hub 3818 is also rotatable about the support shaft 3812 and may berotated by a third rotation means (not shown), such as a motor or thelike. Hubs 3814 and 3818 both contain multiple coating modules 3820,which may be arranged in a cylindrical manner about support shaft 3812.Each coating module 3820 further comprises a series of depositors (bestseen in FIG. 40) extending radially from the support shaft 3812. Thefibers 3806 continuously pass through a set of coating modules 3820 witheach module 3820 synthesizing a predetermined chemistry sequence orcompound onto the fiber. The fibers 3806 pass through both hubs 3814 and3818. Fiber cutting devices 3822 (best seen in FIG. 39) are providedbetween the platform 3808 and hub 3814 and between hubs 3814 and 3818.The fiber cutting devices 3822 sever the fibers 3806 when a newsynthesis sequence or chemical compound is desired. After the fibers3806 pass through both hubs 3814 and 3818, they enter adeprotection/quality-control module 3824 and thereafter are supplied tothe end-product, for example another spool or a fiber array 3826. Amotor 3828 moves the end-product to position multiple fibers thereon. Itshould be appreciated that hubs 3814 and 3818 may be cylindrical or ofany suitable shape.

Corresponding to the circular arrangement of the fiber spools 3804, thecoating modules 3820 are arranged to receive fiber 3806, continuouslysynthesizing one compound onto it, and output the fiber 3806 such thatit can be introduced into an adjacent coating module 3820. For eachfiber 3806, the modules 3820 are stacked on top of one another togenerate the desired synthesis or compound. When a new synthesissequence for the fibers 3806 is desired, the cutting modules 3822 (FIG.39) sever each fiber 3806, and the lower hub 3818 is rotated relative tothe upper hub 3814. This rotation of the lower hub 3818 causes thefibers 3806 from the upper hub 3814 to enter another module in the lowerhub 3818 as the fibers 3806 of cut-length continues to pass through thelower hub 3818. In other words, the motion of fiber 3806 through thesystem is not interrupted to change to a new synthesis sequence. Thefiber may initially be manually fed through the modules, and once thefiber is cut, the fiber from the upper hub may naturally feed into thelower hub after it has rotated. Alternatively, the fiber may be fusedwith the end of an adjacent fiber located in the lower hub after it hasbeen rotated. The fusing of fiber ends may be accomplished bymechanical, chemical or thermal means.

FIG. 39 is an enlarged perspective view of the fiber cutting device 3822illustrated in FIG. 38. The fiber cutting device 3822 consists of a top3902 and bottom 3904 circular saw blades in the location between theplatform 3808 and the upper hub 3814. The top blade 3902 may be fixed tothe motor 3810 that rotates the platform 3808 about the support shaft3812. The bottom blade 3904 may be fixed to the stationary hub 3814.When the platform 3808 rotates to a new position, the fiber cuttingdevice 3822 cuts all the fibers 3806 simultaneously between the platform3808 and the upper hub 3814. A similar fiber cutting device 3822 mayalso be located between hubs 3814 and 3818. The top blade 3902 of thefiber cutting device 3822 may be fixed to the upper hub 3814. The bottomblade 3904 rotates with the lower hub 3818, cutting the fibers 3806 asit rotates.

FIG. 40 is a side view of the coating module illustrated in FIG. 38. Thecoating module 3820 may consist of multiple containers 4002 containingliquids 4004-4016 through which a fiber 3806 may be continuously passed.The fiber 3806 is guided through the liquids 4004-4016 by small rollers4018 and large rollers 4020. The liquids 4004-4016 are of the correctchemical composition and concentration to add a DNA base to the fiber3806. One arrangement of liquids 4004-4016, listed in order of fibercontact, are: detritylation 4004, activator 4006, phosphoramidite (base)4008, capping agent A & B 4010, washing solution 4012, oxidizer 4014,and a second washing solution 4016. The fiber 3806 may exit the coatingmodule 3820 at the same rate that it enters, and at a composition thatallows a subsequent (or the same) module 3820 to chemically add orsynthesize another base onto the DNA chain.

A plurality of modules 3820 can be stacked to add as many DNA bases ontoa fiber 3806 as desired. For example, FIG. 41 shows three modules 4100 -4104 stacked so as to synthesize three bases onto the fiber 3806. Thefiber 3806 is introduced from a spool 3804 that may contain many metersof fiber 3806.

After the bases are synthesized onto the fiber 3806, the fiber 3806passes through a deprotection module 3824 where protection chemicals areremoved. The removal process releases a small percentage of oligos thatare tested by quality control sensors 4108. After deprotection, thefiber 3806 is positioned in channels on a plurality of fiber arraysubstrates 3826. A motor 3828 moves the fiber arrays 3826 such that thefibers fill all of the channels. Cutting means 4110 are provided beforeand between the fiber arrays 3826 to sever the fiber into shortsegments.

FIG. 42 is an enlarged side view of the deprotection module illustratedin FIG. 38. The deprotection module 3824 removes deprotection groups4208 that were added to an oligo 4210 during synthesis. This removal isimplemented by exposing the oligos 4210 to a deprotection composition4212 such as methyl aminine, to dissolve the deprotection groups 4208.In addition, to removing deprotection groups 4208, some of the oligos4218 are extracted from the fiber 3806 for quality control purposes.This removal is implemented by applying two different types of linkersto hold the oligos 4210 onto the fibers 3806, namely cleavable 4214 andpermanent 4216 linkers. The clevable linkers 4214 dissolve during thedeprotection process while the permanent linkers 4216 do not. Most ofthe linkers are may be permanent linkers 4216 such that only a smallpercentage of oligos 4210 are removed from the fiber 3806. The oligos4218 removed will be passed through various quality control sensors2008, such as for example a liquid chromotography column 4202 for puritymeasurement, with an ultraviolet light detector 4204 and a massspectrometer 4206 for identification.

FIG. 43 is an enlarged side view of another embodiment of a coatingmodule 4302. In this configuration, the coating module 4302 isprogrammed to synthesize one of multiple bases solutions 4304-4310, asselected by an operator, onto the fiber 3806. The base solutions may beoglios A, C, G or T. The module 4302 may still contain the detritylation4004, activator 4006, capping agents 4010, wash-one 4012, oxidizer 4014,and wash-two 4016—solutions. However, the module 4302 may additionallycontain a bath for all bases 4304-4310 instead of only a bath containingone base 4008 as described in relation to the first configuration 3820(FIG. 40). The selector 3428 ( shown in FIG. 34) selects one of multipleactuators 4312-4318 to push the fiber 3806 into contact with one of themultiple base solutions 4304-4310, adding that base in the same processas described above. When a different base is desired, the extendedactuator 4312, 4314, 4316 or 4318 is retracted and another actuator4312, 4314, 4316 or 4318 extends the fiber into contact with a differentbase solution 4304-4310. This process is repeated as often as desired tosynthesize an oglionucleotide onto the fiber 3806. This type of coatingmodule 4302 can be stacked as shown in FIG. 44, with fiber spools 3804,deprotection modules 3824, and motor 3828 to lay the fibers 3806 into aplurality of fiber arrays 3826.

One application for the present invention is DNA synthesis, inparticular making every combination of a certain DNA length. Forexample, every combination of a 9 base long DNA fragment (oligo) wouldgenerate 262,144 different oligos (4 to the ninth power). Eight modulesper fiber could generate a 9-base oligo if the fibers are loaded intothe machine with one base already attached (see FIG. 17). However, tomake 262,144 stacks of 8-high modules would be daunting. But, with thisdevice, a relatively small set of modules can be arranged to multiplythe number of different combinations generated. For example, 256 fiberscan be passed through the upper hub with four-modules per fiber tosynthesis every combination of four bases on those fibers (256). If thelower hub is arranged the same way (256 fibers×4 modules), the systemwould synthesize 256, 9-base oligos simultaneously —a small subset ofthe 262,144 combinations required. However, when a subset of fibers ismade, the fibers can be cut, and the lower hub rotated to make a secondsubset of fiber combinations. By repeating this process 256 times,65,536 combinations of a 9-mer will have been synthesized (255×256).Now, the platform is rotated one fiber position and the whole processrepeated another three times to synthesize every 9-mer combination of262,144.

FIGS. 45A and 45B are partial perspective views of a fiber array plate4500, according to an embodiment of the invention. The fiber array plate4500 includes a base 4502, made from a first material, having multiplegrooves 4504 formed therein. In one embodiment, the grooves have asubstantially square cross-section and are substantially parallel to oneanother. However, the grooves 4504 may have any suitable cross-section,such as a rectangular or semi-circular cross-section, and may beoriented to one another in any suitable direction so long as thechannels do not intersect with one another. An upper surface 4508 of thebase 4502 may be substantially flat. The base is formed from a firstmaterial.

The grooves 4504 are substantially filled with a second material to formembedded optical fibers 4506. In one embodiment, the second material maybe more optically transparent than the first material. In particular,the first material may be opaque or reflective, while the secondmaterial may be optically transparent. Alternatively, the first and thesecond materials may both be transparent, but with different refractiveindices chosen to ensure that light is contained within each embeddedoptical fiber 4506.

The upper surface 4510 of each of the embedded optical fibers 4506 maybe substantially flat and flush with the upper surface 4508 of the base4502. Alternatively, the upper surface 4510 of the embedded fibers 4506may extend slightly above the upper surface 4508 of the base 4502. Inaddition, the grooves 4504, and hence the embedded optical fibers 4506,may extend completely across the base 4502, i.e., from edge to edge ofthe base, may extend only partially across the base 4502, or may haveone end flush with an edge of the base and the other end terminatebefore the edge of the base. Also, the upper surfaces 4508 and 4510, aswell as the edges of the base, may be polished or ground to besubstantially flat. Furthermore, in some embodiments, one end of eachembedded optical fiber may be coated with a reflective material.

Once the base with embedded optical fibers has been formed, a chemicalspecies or probe 4512-4518 is then attached to the upper surface 4510 ofeach embedded optical fiber 4506. In one embodiment, each chemicalspecies or probe 4512-4518 attached to the embedded optical fibers 4506is different to the remainder of the probes on a particular fiber arrayplate 4500. Also, the grooves 4504 are spaced sufficiently far from oneanother so that cross-contamination of the probes 4512-4518 does notoccur.

In some embodiments, the probes 4512-4518 are attached to the embeddedoptical fibers 4506 via an inkjet printing technique that uses an inkjetprinting head 4520. However, it should be appreciated to those skilledin the art that any suitable method for attaching a chemical species toa substrate may be employed, such as wicking or the like.

In some embodiments, the chemical species or probe 4512-4518 is attachedto the upper surface 4510 of each embedded optical fiber 4506 all atonce. For example, an oligonucleotide probe may be attached to anoptical fiber. In other embodiments, different chemical species areattached to the optical fibers to synthesize the desired probe. Forexample, one or more monomers are attached to the optical fibers tosynthesize an oligonucleotide.

In use, fiber array plate 4500 is used in combination with a channelplate, as described below in relation to FIGS. 46A and 46B.

FIG. 46A is an isometric view (top view 4600, and side view 4610) of achannel plate 4602. The channel plate 4602 includes a base 4604 withmultiple substantially parallel channels 4606 formed therein. In oneembodiment, each channel 4606 has two distal ends that do not extend allthe way across the base 4604, i.e., terminate before the edges of thebase 4604. One end of each of the channels 4606 may include a well 4608for receiving a chemical species or target solution into each channel.Each alternating channel 4606 may have a well disposed at an oppositeend to the channels adjacent to it. This allows the channels 4606 to bespaced closer to one another, providing for more channels per base 4604.Each well and channel combination allow the target solution received atthe well to freely flow along the channel to the end of the channelremote from the well. Furthermore, the base, with channels and wellsformed therein, may be made from an optically transparent or reflectivematerial based on the position of the detector, as described below inrelation to FIGS. 47 and 48. The optical fiber plate may also beflexible or rigid.

In yet another embodiment, the channel plate 4602 includes a gate strip4609 near both ends of the channels 4606. The gate strip is disposedsubstantially perpendicular to the channels 4606 to temporarily restrictflow of target solutions from the wells along the channels. A gate maybe necessary to prevent the target solutions moving along the channels,as in some embodiments the target solution may be forced along eachchannel using capillary force, which causes the solution to rapidly movealong the channels. Once ready for binding to occur, the gate strip isremoved and the target solutions flow from the wells along the channelsThe gate strip may be removed by an operator, or the gate strip may beremoved automatically by the device or system performing the detection.

FIG. 46B is a perspective view of the fiber array plate 4500 and thechannel plate 4602 of FIGS. 45A and 46A, respectively. In use, the fiberarray plate 4500 is placed into contact with the channel plate 4602,such that the upper surfaces 4510 (FIG. 45A) of the embedded opticalfibers 4506 (FIG. 45A) are exposed to the channels 4606 (FIG. 46A and46B) of the channel plate 4602. In one embodiment, the fiber array plate4500 and the channel plate 4602 are contacted with one another, suchthat the embedded optical fibers 4506 (FIGS. 45A and 45B) are arrangedsubstantially perpendicular to the channels 4606 (FIG. 46A). In this waya matrix of contact positions are formed at each intersection of theembedded optical fibers 4506 (FIGS. 45A and 45B) and the channels 4606(FIG. 46A).

In some embodiments, the combination of the fiber array plate 4500 andthe channel plate 4602 defines multiple enclosed channels having adiameter that is capable of forcing a target solution along the channelsusing a capillary force alone. In these embodiments, each channel may beup to several meters long having a cross-sectional dimension of about100 by 100 microns. In this embodiment, the fiber array plate 4500 maybe permanently affixed to the channel plate 4602, and sold as a singlefiber array.

In use, different target solutions are poured into each well 4608 of thechannel plate 4602 (FIGS. 46A and 46B). The fiber array plate 4500 (FIG.45) is then positioned over the channel plate 4602 such that theembedded optical fibers 4506 (FIG. 45A) are perpendicular to thechannels 4606 (FIG. 46A). The combination of the fiber array plate 4500and the channel plate 4602, collectively referred to below as the fiberarray, is then agitated or each end alternately elevated so that thetarget solutions in the channels 4606 (FIG. 46) move from the wellsalong the channels. Alternatively, a capillary force causes the targetsolutions in the channels 4606 (FIG. 46) move from the wells along thechannels. During such movement, the target solutions make contact withthe fiber array plate 4500. In particular, the target solutions makescontact with the embedded optical fibers of the fiber array plate at theintersection between the channels and the embedded optical fibers. Inthis way each different target solution in each channel contacts adifferent probe attached to each embedded optical fiber.

As described above, binding may occur between a target solution and aprobe. Again, as described above, a light from a light source isdirected towards an end of each of the embedded optical fibers. Thelight may be directed at the optical fibers either simultaneously orsequentially. This light forms an evanescent wave near the surface ofeach embedded optical fiber, as described above. If binding occursbetween a target solution and a probe, the evanescent wave will excite aflorescent dye contained in the target solution or combined with theprobe. This causes more light to be emitted where binding occurs thanwhere no binding occurs. The light emitted is recorded by a detector (asdescribed above) located either under a transparent base 4604 of thechannel plate 4602, above a transparent fiber array plate 4500, orperpendicular to the fiber array and channel plates at an opposite sideof the embedded optical fibers to where the light entered each opticalfiber.

The embodiment of the fiber array that includes the embedded opticalfibers, otherwise known as integrated optics, has many advantages. Forexample, the construction of the fiber array plate is relatively simple,and may be constructed using low cost injection molding techniques orthe like. The addition of the probes can also be performed at low costusing existing printing technologies. Also, the grooves can be filledvery accurately. Furthermore, even if the grooves are not filled veryaccurately, i.e., over or under filled, any uneven surfaces can bepolished flat. In other words, if the mating surfaces of the fiber arrayplate and the channel plate are not perfectly flat, the surfaces can bepolished flat, thereby ensuring a complete mating of surfaces. Thiscomplete mating of surfaces seals the channels, thereby avoiding crosscontamination between channels.

FIG. 47 is a schematic of a fiber array system 4700 that uses molecularbeacons, according to another embodiment of the invention. The use ofmolecular beacons can be used with any of the fiber array systemsdescribed above. Although only one optical fiber 4706 is shown, thefiber array system includes multiple substantially parallel opticalfibers. Each fiber has a different probe chemical species (probe) 4716attached thereto. One end of each optical fiber 4706 is exposed to alight source 4702 while the other is coated with a reflective coating4724. Also, although only two channels 4708 are shown, the fiber arraysystem 4700 may include multiple channels 4708 disposed substantiallyperpendicular to the optical fiber 4706, as described above. Each of themultiple channels is configured to receive a different target solutiontherein. The target solution includes one or more target chemicalspecies 4718.

The fiber array system 4700 also includes a light source 4702, one ormore optical elements 4704 configured to direct light from the lightsource 4702 at one end of an optical fiber 4706, a detector 4712configured to detect light emitted from the fiber array system, andoptical elements 4714 configured to direct light emitted from the fiber4706 into the detector 4712.

Either the probe or target chemical species includes a molecular beaconattached thereto (shown by Q and R). However, for ease of explanation,the molecular beacon will be described as attached to the probe.Generally, molecular beacons are single-stranded oligonucleotidehybridization probes that form a stem-and-loop structure. The loopcontains a probe sequence that is complementary to a target sequence,and the stem is formed by the annealing of complementary arm sequencesthat are located on either side of the probe sequence. A fluorophore orreporter (R), or the like, is covalently linked to the end of one armand a quencher (Q) is covalently linked to the end of the other arm.Molecular beacons do not fluoresce when they have not bound. However,when they hybridize or bind to a complementary target they undergo aconformational change that enables them to fluoresce brightly.

In the absence of targets, the probe is dark, because the stem placesthe fluorophore so close to the nonfluorescent quencher that theytransiently share electrons, eliminating the ability of the fluorophoreto fluoresce. This can be seen at reference numeral 4722. When the probeencounters a target molecule, it forms a probe-target hybrid that islonger and more stable than the stem hybrid. The rigidity and length ofthe probe-target hybrid precludes the simultaneous existence of the stemhybrid. Consequently, the molecular beacon undergoes a spontaneousconformational reorganization that forces the stem hybrid to dissociateand the fluorophore and the quencher to move away from each other,restoring fluorescence, as shown at reference numeral 4720.

In addition, molecular beacons can be synthesized that possessdifferently colored fluorophores, enabling assays to be carried out thatsimultaneously detect different targets or probes in the same reaction.For example, a target solution may contain multiple targets each havinga different molecular beacon, each labeled with a different fluorophoreof a different color, attached thereto. The color of the resultingfluorescence, identifies the target. This enables cost-efficientmultiplex fiber array systems to be developed. Further details onmolecular beacons can be found in Xiaohong Fang and Weihong Tan, AFiber-Optic Evanescent Wave DNA Biosensor Based on Novel MolecularBeacons, 5054-5059 Anal. Chem 71 (1999), the entire contents of whichare incorporated herein by reference.

FIG. 48 is a perspective view of a portable detector 4800, according toanother embodiment of the invention. The portable detector 4800 detectsand analyzes binding between two chemical species. The portable detector4800 is configured and dimensioned to be portable, i.e., easily carriedby hand from place to place. The portable detector 4800 includes ahandle 4820 attached to a portable housing 4802. The portable housing4802 may include a door 4812 for inserting a fiber array into theportable detector 4800. The fiber array may be any of the fiber arraysdescribed above.

In one embodiment, the portable detector 4800 contains a self-containedor internal power-source 4824, such as a rechargeable battery or fuelcell, and requires no external power to operate. Alternatively, theportable detector 4800 may powered by an external power source, such asby inserting an attached power-cord into a standard electrical outlet.In yet another embodiment, the portable detector may be powered by bothan internal power source 4522 or an external power source.

The portable detector 4800 also includes a support 4808 configured anddimensioned to securely hold any of the above described fiber arrays. Inthe embodiment shown in FIG. 48, the fiber array includes a fiber arrayplate 4500 (FIGS. 45A and 45B) and a channel plate 4602 (FIG. 46A). Thesupport 4808 may also include a thermal cycler so that Polymerase ChainReaction (PCR) or amplification can be performed in-situ within theportable detector 4800. The support 4808 may also include an agitatorfor ensuring that target solutions contact the probes on the embeddedoptical fibers. The support plate may also include a heater for thermalcycling or the like.

The portable detector also includes a light source 4810 for directinglight into each of the optical fibers within the fiber array. A suitablelight source may be an excitation laser or an arc lamp. Alternatively,the light source may include a separate Light Emitting Diode (LED) foreach optical fiber to be illuminated. The portable detector 4800 alsoincludes one or more optical elements 4814 for directing light emittedfrom the fiber array toward a detector 4818. A suitable detector 4818may be a solid-state diode or a photo multiplier tube. The portabledetector 4800 may also include: a computing device 4822; motion devices(not shown) to move the detector and/or light source relative to thefiber array, if necessary; and a control panel 4816 for receivingcommands and displaying the results of an assay. Although not shown, thevarious components of the portable detector are coupled to one another,as understood by those skilled in the art. For example, the computingdevice 4822 may be electrically coupled to the support 4808, the lightsource 4810, the detector 4818, the control panel 4816, and the battery4824.

In use, a fiber array with a target solution is placed into the portabledetector 4800 through the door 4812. A system operator then starts thesystem using the control panel 4816. If necessary, the thermal cycler inthe support 4808 performs PCR or amplification. If the fiber arrayincludes a gate, such as the gate 4609 (FIG. 46A), then the portabledetector may automatically remove the gate to initiate movement of thetarget solution along the channels. If present, the(computing device4822 may then instruct the agitator in the support 4808 to beginagitation. Once agitation has completed the computer instructs the lightsource 4810 to illuminate the optical fibers, either simultaneously orsequentially to avoid cross-talk. An evanescent wave is then formed atthe surface of each fiber. If any binding occurs between a target and aprobe, light is emitted towards the detector, which detects the light.The computer then analyses the results of the detection based on thelocation of the known probes and the results are displayed to theoperator via the control panel 4816.

Accordingly, the portable detector 4800 may be used to detect bindingon-site, such as in rural hospitals, or the like. In addition, theportable detector can analyze multiple targets, is flexible, hasmulti-uses, is low cost, and simple to manufacture and operate.

Various embodiments of the invention have been described. Thedescriptions are intended to be illustrative of the present invention.It will be apparent to one of skill in the art that modifications may bemade to the invention as described without departing from the scope ofthe claims set out below. For example, it is to be understood thatalthough the invention has described various geometries for the supportplate and the arrangement of the fibers and channels, other geometriesare possible and are contemplated to fall within the scope of theinvention. Further, although the invention has been illustrated withparticular reference to oligonucleotides and nucleic acid sequencing,any use for contacting at least two chemical species is contemplated tofall within the scope of the invention. The foregoing descriptions ofspecific embodiments of the present invention are presented for purposesof illustration and description. For example, any methods describedherein are merely examples intended to illustrate one way of performingthe invention. They are not intended to be exhaustive or to limit theinvention to the precise forms disclosed. Obviously many modificationsand variations are possible in view of the above teachings. For example,the sequencing by hybridization may be format I, II, or III. Also, anyfigures described herein are not drawn to scale. The embodiments werechosen and described in order to best explain the principles of theinvention and its practical applications, to thereby enable othersskilled in the art to best utilize the invention and various embodimentswith various modifications as are suited to the particular usecontemplated. Furthermore, the order of steps in the method are notnecessarily intended to occur in the sequence laid out. It is intendedthat the scope of the invention be defined by the following claims andtheir equivalents.

1. A device for detecting the binding of two chemical species,comprising: a first plate comprising: a base having multiple groovesformed therein; and multiple optical fibers each disposed within acorresponding one of said multiple grooves; and a second plate havingmultiple channels formed therein, where said first plate and said secondplate are configured to be placed adjacent to one another such that eachsaid optical fiber is exposed to and traverses said multiple channels.2. The device of claim 1, wherein said grooves are substantiallyparallel to one another.
 3. The device of claim 1, wherein said multiplechannels are substantially parallel to one another.
 4. The device ofclaim 1, wherein each of said grooves have a cross-section selected fromthe group consisting of: a square cross-section, a rectangularcross-section, a semicircular cross section, and a mixture thereof. 5.The device of claim 1, wherein each of said grooves have a substantiallysquare cross-section.
 6. The device of claim 1, wherein each of saidoptical fibers substantially occupies said corresponding one of saidmultiple grooves.
 7. The device of claim 1, wherein said base and saidoptical fibers have different refractive indices.
 8. The device of claim1, wherein an upper surface of said base and said optical fibers aresubstantially flush with one another.
 9. The device of claim 1, whereineach optical fiber comprises a different chemical species immobilizedthereon.
 10. The device of claim 1, wherein said optical fibers aresubstantially parallel to one another.
 11. The device of claim 1,wherein said grooves extend across an entire length of said base. 12.The device of claim 1, wherein said channels extend partially across alength of said channel plate.
 13. The device of claim 1, wherein saidchannel plate defines multiple wells, each fluidly coupled to acorresponding channel of said multiple channels.
 14. The device of claim1, wherein said base is opaque.
 15. The device of claim 1, wherein saidbase is reflective.
 16. A method for making a device for detecting thebinding of two chemical species, said method comprising: immobilizingeach of a plurality of known chemical species on a separate opticalfiber of multiple optical fibers each disposed within a correspondingone of multiple grooves formed in a first plate; and placing a secondplate having multiple channels formed therein adjacent to said firstplate such that each said optical fiber is exposed to and traverses saidmultiple channels.
 17. A method for using a device for detecting thebinding of two chemical species, said method comprising: placing asecond plate having multiple channels formed therein adjacent to a firstplate having a plurality of immobilized chemical species eachimmobilized on a separate optical fiber of multiple optical fibers eachdisposed within a corresponding one of multiple grooves formed in thefirst plate, such that each said optical fiber is exposed to andtraverses said multiple channels; and depositing each of a plurality ofmobile chemical species into a separate one of said channels; contactingsaid mobile chemical species with said immobilized chemical species; anddetecting whether binding occurs between at least one of said mobilechemical species and at least one of said immobilized chemical species.18. A portable detector for detecting the binding of two chemicalspecies, the portable detector comprising: a support configured toreceive a fiber array, wherein said fiber array comprises multipleoptical fibers; a light source configured to direct light at an end ofeach of the multiple optical fibers; and a detector configured to detectlight emitted from at least one of the multiple optical fibers caused bybinding of two chemical species.
 19. The detector of claim 18, furthercomprising a housing configured to receive said fiber array therein,wherein said support is disposed within said housing and said lightsource and detector are coupled to said housing.
 20. The detector ofclaim 18, wherein the fiber array comprises a support having multiplechannels therein, wherein the multiple optical fibers are disposed onthe support across the channels, where each of the multiple opticalfibers has an immobilized chemical species thereon.
 21. The detector ofclaim 18, further comprising a power source coupled to said housing. 22.The detector of claim 18, wherein said power source is a battery. 23.The detector of claim 18, wherein said power source is a fuel-cell. 24.The detector of claim 18, further comprising a computing device coupledto said housing and electrically coupled to said detector forcontrolling said binding detection.
 25. The detector of claim 24,wherein said computing device is further configured to receive commandsfor performing a binding assay, controlling the binding assay, anddisplaying results of the binding assay.
 26. The detector of claim 18,further comprising a thermal cycler coupled to said housing forthermally cycling the fiber array.
 27. The detector of claim 18, furthercomprising an agitator for agitating the fiber array.
 28. The detectorof claim 18, further comprising optical elements disposed between saidlight source and the multiple optical fibers.
 29. The detector of claim18, further comprising optical elements disposed between the multipleoptical fibers and said detector.
 30. The detector of claim 18, furthercomprising a computer within said housing for controlling said bindingdetection.
 31. The detector of claim 18, further comprising at least onemotion device coupled to said housing for moving said detector relativeto the fiber array.
 32. The detector of claim 18, further comprising atleast one motion device coupled to said housing for moving said lightsource relative to the fiber array.
 33. A portable detector, configuredto be carried by hand, for detecting the binding of two chemicalspecies, the portable detector comprising: a fiber array comprising: aplate having multiple channels therein; multiple optical fibers disposedon said plate across the channels, where each of the multiple opticalfibers has an immobilized chemical species thereon; a housing configuredto receive said fiber array therein; a light source coupled to saidhousing, wherein said light source is configured to direct light at anend of each of said multiple optical fibers; and a detector coupled tosaid housing, wherein said detector is configured to detect lightemitted from at least one of said multiple optical fibers caused bybinding of two chemical species.
 34. The detector of claim 33, furthercomprising optical elements disposed between said light source and saidmultiple optical fibers, and optical elements disposed between saidmultiple optical fibers and said detector.
 35. A device for contactingat least two chemical species, comprising: a plate comprising a channelcapable of receiving a mobile chemical species; and a fiber having animmobilized chemical species disposed along a portion of said fiber,wherein said fiber is disposed on said plate across a width of saidchannel such that said portion of said fiber is exposed to said channel;and a molecular beacon coupled to said mobile or said immobilizedchemical species.
 36. The device of claim 35, wherein said molecularbeacon is coupled to said immobilized chemical species and comprises asingle-stranded bi-labeled florescent probe held in a hairpin-loopconformation by complementary stem sequences near both ends of saidprobe.
 37. The device of claim 35, wherein said molecular beacon iscoupled to said mobile chemical species and comprises a single-strandedbi-labeled florescent probe held in a hairpin-loop conformation bycomplementary stem sequences near both ends of said probe.
 38. Thedevice of claim 35, wherein said molecular beacon comprises aflorescence reporter.
 39. The device of claim 35, wherein said molecularbeacon comprises a moiety at one end of said immobilized chemicalspecies and a non-florescent quenching moiety at another end of saidimmobilized chemical species.